05 isescan plasmidfinder export pip -i参数 singularity使用安装metawrap phyloflash安装apptainer

本文介绍: 版本更安全，因为它仅允许该程序以其所有者的权限运行，而不允许它以执行者的权限运行。make 编译过程中用到的或者下载下来的文件在哪 go 下载的临时文件都在哪里呢通常在go env GOPATH 路径下面。编译过程中产生的中间文件通常在编译命令执行的当前目录下的中间目录，具体目录名称和编译工具有关。它允许安装、升级和删除软件包。时，当它被执行时，它的权限将从它的所有者变为它的执行者。标记的程序，该程序仍将具有更高的权限，以便完成某些任务。时，该程序仅具有它的所有者的权限，即使它被普通用户执行。

Manual install (install from source code)

Ins t all ISEScan
- Download t h e la test ISEScan from https://github.com/xiezhq/ISEScan/releases, e.g. Sourc e code (tar.gz).
- Uncom p res s t h e .zip (or .tar.gz) file.
  - Use unzip command to uncom p ress t h e zip file:
```
 unzip v1.7.2.2.zip
```
  - Use tar command to uncom p ress t he tar.gz file:
```
 tar -zvxf v1.7.2.2.tar.gz
```
  This will create a ISEScan folder, e.g. ISEScan-1.7.2.2. You need to go to ISEScan folder to configure and run it.
```
 cd ISEScan-1.7.2.2
```
Install de p endenc ies before you run ISEScan
- Python 3.3.3 or later 可以使用 conda 安装挺快
- numpy-1.8.0 or later 这一步不用安装因为在安装 fastcluster时候会自动安装
- sci py-0.13.1 or later 使用 pip in stall -i https://pypi.douban.co m/simple/安装
- fastcluster, latest version recomm ended, fastcluster · PyPI
- FragGeneScan1.30 or ear lier, (The .faa file output by version1.31 is not co m patible with ISEScan!), FragGeneScan
- HMMER-3.1b2 or later, HMMER3.1使用 – 简书 HMMER conda 安装hen’s HMMER
- BLAST 2.2.31 or later
- SSW Library, the latest version is not tested with ISEScan and the tested version of SSW library is shipped with ISEScan, please find it at ssw201507 subdirectory.
  - To use the sh ipped SSW library in ISEScan, please go to ssw201507 and then co m pile the co des by gcc:
```
 cd ssw201507
 gcc -Wall -O3 -pipe -fPIC -shared -rdynamic -o libssw.so ssw.c ssw.h
```
  - And then copy libssw.so and set search path:
```
 cp libssw.so ../
 export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH
```
  In command export LD_LIBRARY_PATH=/home/xiezhq/projects/ISEScan-1.7.2.2:$LD_LIBRARY_PATH, please replace /home/xiezhq/projects/ISEScan-1.7.2.2 with the actual path of libssw.so on your co mputer!
  - The latest SSW library can be found at GitHub – mengyao/Complete-Striped-Smith-Waterman-Library.
- bio python 1.62 or later (req ui red by SSW library)
Add the req ui red packages to your $PATH before you run ISEScan
- Add to $PATH the paths point in g to run_FragGeneScan.pl, phmmer, hm msearch, b lastn, blastp, makeblastdb
```
 export PATH=$PATH:/apps/inst/FragGeneScan1.30:/apps/inst/hmmer-3.3/bin:/apps/inst/ncbi-blast-2.10.0+/bin
```
In command export above, please replace /apps/inst/FragGeneScan1.30, /apps/inst/hmmer-3.3/bin and /apps/inst/ncbi-blast-2.10.0+/bin with the actual paths of FragGeneScan, HMMER and BLAST on your co mputer!

kobas

conda create -n kobas python=2.7
#使用activate激活环境直接安装
conda activate kobas
conda install -c bioconda  kobas==3.0.3

meta genema rk

MetaGeneMark-2-exp/reproduce.pdf at master · gatech-genemark/MetaGeneMark-2-exp · GitHub

$ conda install -c bioconda metaphlan

mgrast

GitHub – MG-RAST/MG-RAST-Tools: Repository of script tools, examples, and contributed code for using the MG-RAST API

motusGitHub – HRGV/phyloFlash: phyloFlash – A pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an illumina (meta)genomic dataset.

nt nr

NR/NT，Taxonomy和RefSeq——三种NCBI常见数据库 – 大漠胡天 – 博客园 (cnblogs.com)

cd ${db}
mk dir -p NCBI_nt && cd NCBI_nt
wget -c “ftp://ftp.ncbi.nlm.nih.g ov/blast/db/nt.*.tar.gz”

mkdir -p NCBI_nr && cd NCBI_nr

phylo flash 从头安装

YAMDA/README.md at master · daquang/YAMDA · GitHub

conda install -c bioconda pybedtools

phyloFlash | phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore the phylogenetic composition of an Illumina (meta)genomic dataset.

https://github.com/daquang/YAMDA/blob/master/README.md

bioinformatics-cafe/fastaFromBed at master · dariober/bioinformatics-cafe · GitHub

3、添入环境变量

echo ‘export PATH=~/.aspera/connect/bin/:$PATH’ >> ~/.bashrc
source ~/.bashrc

plasflow 自建频道自建channel

https://github.com/smaegol/PlasFlow

smaegol :: Anaconda.org

qiime2

Conda安装qiime2（目前最有效的方法） – 简书

QIIME 2 command-line interface (q2cli) — QIIME 2 2022.11.1 documentation

QIIME 2

Installing QIIME 2 — QIIME 2 2022.11.1 documentation

signalp5 signalp6

Signalp6 :: Anaconda.org

Services- DTU Health Tech

Signalp5 :: Anaconda.org

GitHub – chenxi-zhang-art/signalP

tar –xzvf signalp-5.0b.Linux.tar.gz
https://github.com/fteufel/signalp-6.0/blob/main/installation_instructions.md

Description
A placeholder package for SignalP v5.

Due to license restrictions, this recipe cannot distribute signalp5 directly. Please download signalp-5.0b.Linux.tar.gz from: https://services.healthtech.dtu.dk/services/SignalP-5.0b/9-Downloads.php#

and run the following command to complete the installation:

$ signalp5-register signalp-5.0b.Linux.tar.gz
This will copy signalp5 into your conda environment.

pip install signalp-6-package/ -i https://pypi.douban.com/
simple/

plasmid finder

https://github.com/kcri-tz/plasmidfinder

魔鬼报错

conda install -c bioconda -c conda-for
ge plasmidfinderCollecting package metadata (current_repodata.json): done
Solving environment: done

## Package Plan ##

  environment location: /share/app/miniconda3/envs/plasmidfinder

  added / updated specs:
    - plasmidfinder


The following packages will be downloaded:

    package                    |            build
    ---------------------------|-----------------
    biopython-1.80             |  py311hd4cff14_0         2.9 MB  conda-forge
    boost-1.80.0               |  py311h59ea3da_4         358 KB  conda-forge
    boost-cpp-1.80.0           |       h75c5d50_0        17.4 MB  conda-forge
    cgecore-1.5.6              |     pyh3252c3a_0          34 KB  bioconda
    kma-1.4.9                  |       h7132678_0         261 KB  bioconda
    numpy-1.24.2               |  py311h8e6699e_0         7.4 MB  conda-forge
    plasmidfinder-2.1.6        |  py310hdfd78af_1         1.7 MB  bioconda
    tabulate-0.9.0             |     pyhd8ed1ab_1          35 KB  conda-forge
    ------------------------------------------------------------
                                           Total:        30.1 MB

The following NEW packages will be INSTALLED:

  _libgcc_mutex      conda-forge/linux-64::_libgcc_mutex-0.1-conda_forge 
  _openmp_mutex      conda-forge/linux-64::_openmp_mutex-4.5-2_gnu 
  biopython          conda-forge/linux-64::biopython-1.80-py311hd4cff14_0 
  blast              bioconda/linux-64::blast-2.5.0-hc0b0e79_3 
  boost              conda-forge/linux-64::boost-1.80.0-py311h59ea3da_4 
  boost-cpp          conda-forge/linux-64::boost-cpp-1.80.0-h75c5d50_0 
  bzip2              conda-forge/linux-64::bzip2-1.0.8-h7f98852_4 
  ca-certificates    conda-forge/linux-64::ca-certificates-2022.12.7-ha878542_0 
  cgecore            bioconda/noarch::cgecore-1.5.6-pyh3252c3a_0 
  icu                conda-forge/linux-64::icu-70.1-h27087fc_0 
  kma                bioconda/linux-64::kma-1.4.9-h7132678_0 
  ld_impl_linux-64   conda-forge/linux-64::ld_impl_linux-64-2.40-h41732ed_0 
  libblas            conda-forge/linux-64::libblas-3.9.0-16_linux64_openblas 
  libcblas           conda-forge/linux-64::libcblas-3.9.0-16_linux64_openblas 
  libffi             conda-forge/linux-64::libffi-3.4.2-h7f98852_5 
  libgcc-ng          conda-forge/linux-64::libgcc-ng-12.2.0-h65d4601_19 
  libgfortran-ng     conda-forge/linux-64::libgfortran-ng-12.2.0-h69a702a_19 
  libgfortran5       conda-forge/linux-64::libgfortran5-12.2.0-h337968e_19 
  libgomp            conda-forge/linux-64::libgomp-12.2.0-h65d4601_19 
  liblapack          conda-forge/linux-64::liblapack-3.9.0-16_linux64_openblas 
  libnsl             conda-forge/linux-64::libnsl-2.0.0-h7f98852_0 
  libopenblas        conda-forge/linux-64::libopenblas-0.3.21-pthreads_h78a6416_3 
  libsqlite          conda-forge/linux-64::libsqlite-3.40.0-h753d276_0 
  libstdcxx-ng       conda-forge/linux-64::libstdcxx-ng-12.2.0-h46fd767_19 
  libuuid            conda-forge/linux-64::libuuid-2.32.1-h7f98852_1000 
  libzlib            conda-forge/linux-64::libzlib-1.2.13-h166bdaf_4 
  ncurses            conda-forge/linux-64::ncurses-6.3-h27087fc_1 
  numpy              conda-forge/linux-64::numpy-1.24.2-py311h8e6699e_0 
  openssl            conda-forge/linux-64::openssl-3.0.7-h0b41bf4_2 
  pip                conda-forge/noarch::pip-23.0-pyhd8ed1ab_0 
  plasmidfinder      bioconda/noarch::plasmidfinder-2.1.6-py310hdfd78af_1 
  python             conda-forge/linux-64::python-3.11.0-he550d4f_1_cpython 
  python_abi         conda-forge/linux-64::python_abi-3.11-3_cp311 
  readline           conda-forge/linux-64::readline-8.1.2-h0f457ee_0 
  setuptools         conda-forge/noarch::setuptools-67.1.0-pyhd8ed1ab_0 
  tabulate           conda-forge/noarch::tabulate-0.9.0-pyhd8ed1ab_1 
  tk                 conda-forge/linux-64::tk-8.6.12-h27826a3_0 
  tzdata             conda-forge/noarch::tzdata-2022g-h191b570_0 
  wheel              conda-forge/noarch::wheel-0.38.4-pyhd8ed1ab_0 
  xz                 conda-forge/linux-64::xz-5.2.6-h166bdaf_0 
  zlib               conda-forge/linux-64::zlib-1.2.13-h166bdaf_4 
  zstd               conda-forge/linux-64::zstd-1.5.2-h3eb15da_6 


Proceed ([y]/n)? y


Downloading and Extracting Packages
                                                                                                          
                                                                                                          
CondaError: Downloaded bytes did not match Content-Length                                                 
  url: https://conda.anaconda.org/conda-forge/linux-64/numpy-1.24.2-py311h8e6699e_0.conda                 
  target_path: /share/app/miniconda3/pkgs/numpy-1.24.2-py311h8e6699e_0.conda                              
  Content-Length: 7720502                                                                                 
  downloaded bytes: 6650303                                                                               
                                                                                                          
CondaHTTPError: HTTP 000 CONNECTION FAILED for url <https://conda.anaconda.org/conda-forge/linux-64/boost-
cpp-1.80.0-h75c5d50_0.tar.bz2>Elapsed: -

An HTTP error occurred when trying to retrieve this URL.
HTTP errors are often intermittent, and a simple retry will get you on your way.


(plasmidfinder) root@mgt:/share/app/miniconda3/envs/arg/conda-meta# conda install -c bioconda -c conda-for
ge plasmidfinderCollecting package metadata (current_repodata.json): failed

# >>>>>>>>>>>>>>>>>>>>>> ERROR REPORT <<<<<<<<<<<<<<<<<<<<<<

    Traceback (most recent call last):
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 761, in _update_
chunk_length        self.chunk_left = int(line, 16)
    ValueError: invalid literal for int() with base 16: b''
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 444, in _error_c
atcher        yield
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 828, in read_chu
nked        self._update_chunk_length()
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 765, in _update_
chunk_length        raise InvalidChunkLength(self, line)
    urllib3.exceptions.InvalidChunkLength: InvalidChunkLength(got length b'', 0 bytes read)
    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 816, in generate
        yield from self.raw.stream(chunk_size, decode_content=True)
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 624, in stream
        for line in self.read_chunked(amt, decode_content=decode_content):
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 816, in read_chu
nked        with self._error_catcher():
      File "/share/app/miniconda3/lib/python3.10/contextlib.py", line 153, in __exit__
        self.gen.throw(typ, value, traceback)
      File "/share/app/miniconda3/lib/python3.10/site-packages/urllib3/response.py", line 461, in _error_c
atcher        raise ProtocolError("Connection broken: %r" % e, e)
    urllib3.exceptions.ProtocolError: ("Connection broken: InvalidChunkLength(got length b'', 0 bytes read
)", InvalidChunkLength(got length b'', 0 bytes read))    
    During handling of the above exception, another exception occurred:
    
    Traceback (most recent call last):
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/exceptions.py", line 1118, in __call_
_        return func(*args, **kwargs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/main.py", line 69, in main_subshe
ll        exit_code = do_call(args, p)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/conda_argparse.py", line 91, in d
o_call        return getattr(module, func_name)(args, parser)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/notices/core.py", line 109, in wrappe
r        return func(*args, **kwargs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/main_install.py", line 20, in exe
cute        install(args, parser, 'install')
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/cli/install.py", line 264, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 136, in solve_fo
r_transaction        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 179, in solve_fo
r_diff        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 284, in solve_fi
nal_state        ssc = self._collect_all_metadata(ssc)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/common/io.py", line 84, in decorated
        return f(*args, **kwds)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 451, in _collect
_all_metadata        index, r = self._prepare(prepared_specs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/solve.py", line 1061, in _prepar
e        reduced_index = get_reduced_index(self.prefix, self.channels,
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/index.py", line 272, in get_redu
ced_index        new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 142, in qu
ery_all        result = tuple(concat(executor.map(subdir_query, channel_urls)))
      File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 621, in result_iterato
r        yield _result_or_cancel(fs.pop())
      File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 319, in _result_or_can
cel        return fut.result(timeout)
      File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 458, in result
        return self.__get_result()
      File "/share/app/miniconda3/lib/python3.10/concurrent/futures/_base.py", line 403, in __get_result
        raise self._exception
      File "/share/app/miniconda3/lib/python3.10/concurrent/futures/thread.py", line 58, in run
        result = self.fn(*self.args, **self.kwargs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 131, in <l
ambda>        subdir_query = lambda url: tuple(
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 147, in qu
ery        self.load()
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 213, in lo
ad        _internal_state = self._load()
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 303, in _l
oad        raw_repodata_str = fetch_repodata_remote_request(
      File "/share/app/miniconda3/lib/python3.10/site-packages/conda/core/subdir_data.py", line 571, in fe
tch_repodata_remote_request        resp = session.get(
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 600, in get
        return self.request("GET", url, **kwargs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 587, in request
        resp = self.send(prep, **send_kwargs)
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/sessions.py", line 745, in send
        r.content
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 899, in content
        self._content = b"".join(self.iter_content(CONTENT_CHUNK_SIZE)) or b""
      File "/share/app/miniconda3/lib/python3.10/site-packages/requests/models.py", line 818, in generate
        raise ChunkedEncodingError(e)
    requests.exceptions.ChunkedEncodingError: ("Connection broken: InvalidChunkLength(got length b'', 0 by
tes read)", InvalidChunkLength(got length b'', 0 bytes read))
`$ /share/app/miniconda3/bin/conda install -c bioconda -c conda-forge plasmidfinder`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=plasmidfinder
                CONDA_EXE=/share/app/miniconda3/bin/conda
             CONDA_PREFIX=/share/app/miniconda3/envs/plasmidfinder
           CONDA_PREFIX_1=/share/app/miniconda3
           CONDA_PREFIX_2=/share/app/miniconda3/envs/motus
           CONDA_PREFIX_3=/share/app/miniconda3/envs/phyloflash
           CONDA_PREFIX_4=/share/app/miniconda3
           CONDA_PREFIX_5=/share/app/miniconda3/envs/plasflow
    CONDA_PROMPT_MODIFIER=(plasmidfinder)
         CONDA_PYTHON_EXE=/share/app/miniconda3/bin/python
               CONDA_ROOT=/share/app/miniconda3
              CONDA_SHLVL=6
           CURL_CA_BUNDLE=<not set>
     JAVA_LD_LIBRARY_PATH=:-:-:-:-:-:-:-
          LD_LIBRARY_PATH=/public/arg/ISEScan-1.7.2.3:/public/arg/ISEScan-1.7.2.3:
               LD_PRELOAD=<not set>
                  MANPATH=/opt/xcat/share/man::/usr/bin/ypuser/man
               MODULEPATH=/share/modulefiles:/root/modulefiles:/usr/share/Modules/modulefiles:/s
                          hare/app/oneapi2022/modulefiles
                     PATH=/public/arg/phyloFlash-
                          pf3.4:/public/arg/FragGeneScan:/public/nanoplot/ncbi-blast-
                          2.13.0+/bin:/public/nanoplot/centrifuge-1.0.3-
                          beta:/public/nanoplot/sratoolkit.2.10.8-
                          centos_linux64/bin:/public/metagenome/microbiome_helper-master:/share/
                          app/miniconda3/envs/plasmidfinder/bin:/public/arg/FragGeneScan:/public
                          /nanoplot/ncbi-blast-2.13.0+/bin:/public/nanoplot/centrifuge-1.0.3-
                          beta:/public/nanoplot/sratoolkit.2.10.8-
                          centos_linux64/bin:/public/metagenome/microbiome_helper-master:/share/
                          app/miniconda3/bin:/share/app/miniconda3/condabin:/share/app/miniconda
                          3/bin:/opt/xcat/bin:/opt/xcat/sbin:/opt/xcat/share/xcat/tools:/usr/lib
                          64/qt-
                          3.3/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/usr/bin/ypu
                          ser:/root/bin
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : plasmidfinder
    active env location : /share/app/miniconda3/envs/plasmidfinder
            shell level : 6
       user config file : /root/.condarc
 populated config files : 
          conda version : 22.11.1
    conda-build version : not installed
         python version : 3.10.9.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.17=0
                          __linux=3.10.0=0
                          __unix=0=0
       base environment : /share/app/miniconda3  (writable)
      conda av data dir : /share/app/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          https://conda.anaconda.org/conda-forge/linux-64
                          https://conda.anaconda.org/conda-forge/noarch
                          https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /share/app/miniconda3/pkgs
                          /root/.conda/pkgs
       envs directories : /share/app/miniconda3/envs
                          /root/.conda/envs
               platform : linux-64
             user-agent : conda/22.11.1 requests/2.28.1 CPython/3.10.9 Linux/3.10.0-1160.el7.x86_64 centos
/7.9.2009 glibc/2.17                UID:GID : 0:0
             netrc file : None
           offline mode : False


An unexpected error has occurred. Conda has prepared the above report.

If submitted, this report will be used by core maintainers to improve
future releases of conda.
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virsorter

GitHub – jiarong/VirSorter2: customizable pipeline to identify viral sequences from (meta)genomic data

Virsorter :: Anaconda.org

"Collecting package metadata (current_repodata.json): done" 表示 conda 正在收集当前存储库中的软件包元数据。元数据包括软件包的版本，依赖关系等信息，conda 需要这些信息来确定如何安装该软件包。

"Solving environment: failed with initial frozen solve. Retrying with flexible solve." 意味着 conda 在初始冻结的解决方案中失败了，因此在使用更加灵活的解决方案时再次尝试安装。这种情况通常表示与当前环境中的软件包冲突，导致 conda 无法安装 mamba。

在这种情况下，建议您创建一个新的 conda 环境，并在该环境中安装该软件包，以避免与当前环境中的软件包冲突。您可以使用以下命令创建新环境：

Option 2 (development version)

The development version is most updated. To install the development version:

conda create -n vs2 -c conda-forge -c bioconda "python>=3.6" scikit-learn=0.22.1 imbalanced-learn pandas seaborn hmmer==3.3 prodigal screed ruamel.yaml "snakemake>=5.18,<=5.26" click mamba
conda activate vs2
git clone https://github.com/jiarong/VirSorter2.git
cd VirSorter2
pip install -e .

apptainer singularity centos 系统

Getting Started | Apptainer

apptainer/INSTALL.md at main · apptainer/apptainer · GitHub

CentOS 7安装Development Tools失败 – 简书

sudo yum groupinstall -y 'Development Tools'

On CentOS/RHEL:

# Install basic tools for compiling
sudo yum groupinstall -y 'Development Tools'
# Ensure EPEL repository is available
sudo yum install -y epel-release
# Install RPM packages for dependencies
sudo yum install -y 
    libseccomp-devel 
    squashfs-tools 
    squashfuse 
    fuse-overlayfs 
    fakeroot 
    /usr/*bin/fuse2fs 
    cryptsetup 
    wget git

Downloads – The Go Programming Language

udo tar -C /usr/local -xzf /tmp/go1.20.linux-amd64.tar.gz 什么意思
The sudo tar -C /usr/local -xzf /tmp/go1.20.linux-amd64.tar.gz command has the following meaning:

sudo: The command is executed with superuser (root) privileges.
tar: The tar (tape archive) command is used to extract files from a tar archive.
-C /usr/local: The -C option specifies the directory (/usr/local) where the tar archive should be extracted.
-xzf: The -x option extracts the files, the -z option uncompresses the archive using gzip, and the -f option specifies the archive file name (/tmp/go1.20.linux-amd64.tar.gz).
So, the overall effect of the command is to extract the contents of the /tmp/go1.20.linux-amd64.tar.gz archive to the /usr/local directory.

git clone —recursive https://github.com/apptainer/apptainer.git 需要加recursive比较稳妥

Clone the repo
With the adoption of Go modules you no longer need to clone the Apptainer repository to a specific location.

Clone the repository with git in a location of your choice:

git clone https://github.com/apptainer/apptainer.git
cd apptainer
By default your clone will be on the main branch which is where development of Apptainer happens. To build a specific version of Apptainer, check out a release tag before compiling, for example:

git checkout v1.1.5
Compiling Apptainer
You can configure, build, and install Apptainer using the following commands:

./mconfig
cd ./builddir
make
sudo make install

（Linux）make编译用法简述_漠效的博客-CSDN博客_make编译

make编译过程中用到的或者下载下来的文件在哪

【1】make
等同于 make all

它是一个解释makefile中指令的命令工具

执行make时，默认会去(当前文件夹下),找名为Makefile的文件

根据Makefile文件来编译源代码，生成目标文件及可执行文件

在每次使用make时,都会重新生成objects，新产生的object会覆盖旧的objects

【2】make clean
清除以前的make命令编译后所产生的object文件(即后缀为“.o”的文件)及其生成的可执行文件

一般来说，在每次使用make时,都会重新生成objects，新产生的object会覆盖旧的objects

但是实际用时，经过多次编译后，必须使用make clean（直接make，以前留下来的错误不能清除干净）

【3】make install
将编译成功的可执行文件移动到make编译时填写的目录，依据生成的makefile文件

一般默认系统目录/usr/local/bin

【4】make dist
产生发布软件包.

即将可执行文件及相关文件打包成一个tar.gz格式的压缩文件，会在当前目录下生成XXX.tar.gz的文件

【5】make distcheck
相当于make dist命令的进化版

生成发布软件包并对其进行检查，以确定发布包的正确性

它会自动把压缩包文件解开，然后执行configure命令，并且执行make，来确认编译不出现错误，并会在最后提示你软件包是否正确

【6】make distclean
类似于make clean

清除以前的make命令编译后所产生的object文件(即后缀为“.o”的文件)及其生成的可执行文件，并将configure生成的文件全部删除掉

通常在使用make clean后使用，清理的更干净，避免影响再次编译

makefile概念
makefile有些类似于脚本，通过定义了一系列的规则，指定哪些文件需要先编译，哪些文件需要后编译，哪些文件需要重新编译，甚至于进行更复杂的功能操作，并且它也可以执行操作系统的命令

当编译安装源码包时，使用make编译，它会默认找当前目录下的makefile文件，依据makefile中的规则，执行编译安装

makefile可以实现自动化编译,原理上来说，只需要一个make命令，整个工程完全自动编译，极大的提高了软件开发的效率

makefile成为了一种被广泛应用于在工程方面的编译方法
————————————————
版权声明：本文为CSDN博主「漠效」的原创文章，遵循CC 4.0 BY-SA版权协议，转载请附上原文出处链接及本声明。
原文链接：https://blog.csdn.net/gx_1_11_real/article/details/81068412

at Makefile 
#
# Non-recursive Makefile GENERATED by `mconfig' -- Wed Feb  8 02:10:40 CST 2023
# configured: /public/arg/apptainer/mconfig --with-suid
#

# [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/base.mk ] #

# silent build
V := @

# source/build locations
BUILDDIR := .
BUILDDIR_ABSPATH := /public/arg/apptainer/builddir
SOURCEDIR := /public/arg/apptainer
SCRIPTSDIR := /public/arg/apptainer/mlocal/scripts
CONTRIBDIR := 
PREFIX := /usr/local
EXECPREFIX := /usr/local
BINDIR := /usr/local/bin
SBINDIR := /usr/local/sbin
LIBEXECDIR := /usr/local/libexec
DATAROOTDIR := /usr/local/share
DATADIR := /usr/local/share
SYSCONFDIR := /usr/local/etc
SHAREDSTATEDIR := /usr/local/com
LOCALSTATEDIR := /usr/local/var
RUNSTATEDIR := /usr/local/var/run
INCLUDEDIR := /usr/local/include
OLDINCLUDEDIR := /usr/include
DOCDIR := /usr/local/share/doc/apptainer
INFODIR := /usr/local/share/info
HTMLDIR := /usr/local/share/doc/apptainer
DVIDIR := /usr/local/share/doc/apptainer
PDFDIR := /usr/local/share/doc/apptainer
PSDIR := /usr/local/share/doc/apptainer
LIBDIR := /usr/local/lib
LOCALEDIR := /usr/local/share/locale
MANDIR := /usr/local/share/man
RPMPREFIX:=

NAME := apptainer
SHORT_VERSION := 1.1.5
VERSION := 1.1.5

HOSTAR := ar
HOSTCC := cc
HOSTCXX := c++
HOSTLD := cc
HOSTRANLIB := ranlib
HOSTSIZE := size
HOSTOBJCOPY := objcopy

AR := ar
CC := cc
CXX := c++
LD := ld
RANLIB := ranlib
SIZE := size
OBJCOPY := objcopy

ARCH := x86_64

CFLAGS :=  -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -fstack-protector --param ssp-buffer-size=4 -Wal
l -Werror -Wfatal-errors -Wno-unknown-warning-option -Wstrict-prototypes -Wpointer-arith -Wbad-function-cast -Woverlength-strings -Wframe-larger-than=2047 -Wno-sign-compare -Wclobbered -Wempty-body -Wmissing-parameter-type -Wtype-limits -Wunused-parameter -Wunused-but-set-parameter -Wno-discarded-qualifiers -Wno-incompatible-pointer-types -pipe -fmessage-length=0 -fPIC
GO := /usr/local/go/bin/go

CGO_CFLAGS := -I/public/arg/apptainer/builddir 
CGO_LDFLAGS := 
CGO_CPPFLAGS := 
CGO_CXXFLAGS := 
export CGO_CFLAGS CGO_LDFLAGS CGO_CPPFLAGS CGO_CXXFLAGS
LDFLAGS := 

# make sure `all' is the first rule
all:

# [ Embedding file :  /public/arg/apptainer/mlocal/frags/common_opts.mk ] #

# a list of extra files to clean augmented by each module (*.mconf) file
CLEANFILES :=

# general build-wide compile options
AFLAGS := -g

LDFLAGS += -Wl,-z,relro,-z,now

# [ Embedding file : /public/arg/apptainer/mlocal/frags/go_common_opts.mk ] #

# go tool default build options
GO111MODULE := on
GO_TAGS := containers_image_openpgp sylog oci_engine apptainer_engine fakeroot_engine
GO_TAGS_SUID := containers_image_openpgp sylog apptainer_engine fakeroot_engine
GO_LDFLAGS :=
# Need to use non-pie build on ppc64le
# https://github.com/apptainer/singularity/issues/5762
# Need to disable race detector on ppc64le
# https://github.com/apptainer/singularity/issues/5914
uname_m := $(shell uname -m)
ifeq ($(uname_m),ppc64le)
GO_BUILDMODE := -buildmode=default
GO_RACE :=
else
GO_BUILDMODE := -buildmode=pie
GO_RACE := -race
endif
GO_MODFLAGS := $(if $(wildcard $(SOURCEDIR)/vendor/modules.txt),-mod=vendor,-mod=readonly)
GO_MODFILES := $(SOURCEDIR)/go.mod $(SOURCEDIR)/go.sum
GOFLAGS := $(GO_MODFLAGS) -trimpath
GOPROXY := https://proxy.golang.org

export GOFLAGS GO111MODULE GOPROXY

# [ Embedding file : /public/arg/apptainer/mlocal/frags/go_unix_opts.mk ] #

GO_TAGS += apparmor selinux
GO_TAGS_SUID += apparmor selinux

# [ Embedding file : /public/arg/apptainer/mlocal/frags/go_runtime_opts.mk ] #

CGO_CFLAGS += -O2 -D_FORTIFY_SOURCE=2 -Wformat -Wformat-security -fstack-protector --param ssp-buffer-size
=4
# [ Embedding file : /public/arg/apptainer/mlocal/frags/release_opts.mk ] #

CFLAGS += -O2
LDFLAGS += -s

# [ Embedding file : /public/arg/apptainer/mlocal/frags/go_normal_opts.mk ] #

# This tells go's link command to add a GNU Build Id, needed for later
#   symbol stripping for example as is done by rpmbuild.
GO_LDFLAGS += -ldflags="-B 0x`head -c20 /dev/urandom|od -An -tx1|tr -d ' n'`"

# [ Embedding file : /public/arg/apptainer/mlocal/frags/arch_x86_64_opts.mk ] #


# [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/combined-mconfsready.mk ] #

# object files list
_OBJ := 

# suffix rules (metarules missing from most variants)


# [ Embedding file : /public/arg/apptainer/builddir/makeit-intermediate/all.mk ] #

all: $()

CLEANFILES += 

# [ Embedding file :    /public/arg/apptainer/mlocal/frags/build_cli.mk ] #

# This file contains all of the rules for building the apptainer CLI binary

# apptainer build config
apptainer_build_config := $(SOURCEDIR)/internal/pkg/buildcfg/config.go
$(apptainer_build_config): $(BUILDDIR)/config.h $(SOURCEDIR)/scripts/go-generate
	$(V)rm -f $(apptainer_build_config)
	$(V) cd $(SOURCEDIR)/internal/pkg/buildcfg && $(SOURCEDIR)/scripts/go-generate

CLEANFILES += $(apptainer_build_config)

# contain apptainer_SOURCE variable list
apptainer_deps := $(BUILDDIR_ABSPATH)/apptainer.deps

-include $(apptainer_deps)

$(apptainer_deps): $(GO_MODFILES)
	@echo " GEN GO DEP" $@
	$(V)$(SOURCEDIR)/makeit/gengodep -v3 "$(GO)" "apptainer_SOURCE" "$(GO_TAGS)" "$@" "$(SOURCEDIR)/cmd
/apptainer"
# Look at dependencies file changes via apptainer_deps
# because it means that a module was updated.
apptainer := $(BUILDDIR)/apptainer
$(apptainer): $(apptainer_build_config) $(apptainer_deps) $(apptainer_SOURCE)
	@echo " GO" $@; echo "    [+] GO_TAGS" "$(GO_TAGS)"
	$(V)$(GO) build $(GO_MODFLAGS) $(GO_BUILDMODE) -tags "$(GO_TAGS)" $(GO_LDFLAGS) 
		-o $(BUILDDIR)/apptainer $(SOURCEDIR)/cmd/apptainer

apptainer_INSTALL := $(DESTDIR)$(BINDIR)/apptainer
$(apptainer_INSTALL): $(apptainer)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $(@D)
	$(V)install -m 0755 $(apptainer) $(apptainer_INSTALL) # set cp to install

singularity_INSTALL := $(DESTDIR)$(BINDIR)/singularity
$(singularity_INSTALL):
	@echo " INSTALL" $@
	$(V)ln -sf apptainer $(singularity_INSTALL)

CLEANFILES += $(apptainer)
INSTALLFILES += $(apptainer_INSTALL) $(singularity_INSTALL)
ALL += $(apptainer)


# bash_completion files
bash_completion1 :=  $(BUILDDIR)/etc/bash_completion.d/apptainer
bash_completion2 :=  $(BUILDDIR)/etc/bash_completion.d/singularity
bash_completions := $(bash_completion1) $(bash_completion2)
$(bash_completions): $(apptainer_build_config)
	@echo " GEN" $@
	$(V)rm -f $@
	$(V)mkdir -p $(@D)
	$(V)$(GO) run $(GO_MODFLAGS) -tags "$(GO_TAGS)" 
		$(SOURCEDIR)/cmd/bash_completion/bash_completion.go $@

bash_completion1_INSTALL := $(DESTDIR)$(DATADIR)/bash-completion/completions/apptainer
bash_completion2_INSTALL := $(DESTDIR)$(DATADIR)/bash-completion/completions/singularity
bash_completions_INSTALL := $(bash_completion1_INSTALL) $(bash_completion2_INSTALL)
$(bash_completion1_INSTALL): $(bash_completion1)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $(@D)
	$(V)install -m 0644 $< $@

$(bash_completion2_INSTALL): $(bash_completion2)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $(@D)
	$(V)install -m 0644 $< $@

CLEANFILES += $(bash_completions)
INSTALLFILES += $(bash_completions_INSTALL)
ALL += $(bash_completions)


# apptainer.conf file
config := $(BUILDDIR)/apptainer.conf
config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/apptainer.conf
# override this to empty to avoid merging old configuration settings
old_config := $(config_INSTALL)

$(config): $(apptainer)
	@echo " GEN $@`if [ -n "$(old_config)" ]; then echo " from $(old_config)"; fi`"
	$(V)$(apptainer) confgen $(old_config) $(config)

$(config_INSTALL): $(config)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $(@D)
	$(V)install -m 0644 $< $@

INSTALLFILES += $(config_INSTALL)
ALL += $(config)

# remote config file
remote_config := $(SOURCEDIR)/etc/remote.yaml

remote_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/remote.yaml
$(remote_config_INSTALL): $(remote_config)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $(@D)
	$(V)install -m 0644 $< $@

INSTALLFILES += $(remote_config_INSTALL)

man_pages := $(BUILDDIR)$(MANDIR)/man1
$(man_pages): apptainer
	@echo " MAN" $@
	mkdir -p $@
	$(V)$(GO) run $(GO_MODFLAGS) -tags "$(GO_TAGS)" 
		$(SOURCEDIR)/cmd/docs/docs.go man --dir $@
	$(V)cd $@;							
		for M in apptainer*; do					
			S="`echo $$M|sed 's/apptainer/singularity/'`";	
			ln -fs $$M $$S;					
		done

man_pages_INSTALL := $(DESTDIR)$(MANDIR)/man1
$(man_pages_INSTALL): $(man_pages)
	@echo " INSTALL" $@
	$(V)umask 0022 && mkdir -p $@
	$(V)install -m 0644 -t $@ $(man_pages)/*

INSTALLFILES += $(man_pages_INSTALL)
ALL += $(man_pages)

# [ Embedding file : /public/arg/apptainer/mlocal/frags/build_network.mk ] #

# This file contains rules for building CNI plugins which can enable
#   different networking functions between container(s) and the host

apptainer_REPO := github.com/apptainer/apptainer

cni_builddir := $(BUILDDIR_ABSPATH)/cni
cni_install_DIR := $(DESTDIR)$(LIBEXECDIR)/apptainer/cni
cni_plugins := $(shell grep '^	_' $(SOURCEDIR)/internal/pkg/runtime/engine/apptainer/plugins_linux.go | c
ut -d" -f2)cni_plugins_EXECUTABLES := $(addprefix $(cni_builddir)/, $(notdir $(cni_plugins)))
cni_plugins_INSTALL := $(addprefix $(cni_install_DIR)/, $(notdir $(cni_plugins)))
cni_config_LIST := $(SOURCEDIR)/etc/network/00_bridge.conflist 
                   $(SOURCEDIR)/etc/network/10_ptp.conflist 
                   $(SOURCEDIR)/etc/network/20_ipvlan.conflist 
                   $(SOURCEDIR)/etc/network/30_macvlan.conflist 
                   $(SOURCEDIR)/etc/network/40_fakeroot.conflist
cni_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/network

.PHONY: cniplugins
cniplugins:
	$(V)umask 0022 && mkdir -p $(cni_builddir)
	$(V)for p in $(cni_plugins); do 
		name=`basename $$p`; 
		cniplugin=$(cni_builddir)/$$name; 
		if [ ! -f $$cniplugin ]; then 
			echo " CNI PLUGIN" $$name; 
		$(GO) build $(GO_MODFLAGS) $(GO_BUILDMODE) -tags "$(GO_TAGS)" $(GO_LDFLAGS) 
			-o $$cniplugin $$p; 
		fi 
	done

# run-singularity script
run_singularity := $(SOURCEDIR)/scripts/run-singularity

run_singularity_INSTALL := $(DESTDIR)$(BINDIR)/run-singularity
$(run_singularity_INSTALL): $(run_singularity)
   @echo ” INSTALL” $@
   $(V)umask 0022 && mkdir -p $(@D)
   $(V)install -m 0755 $< $@

INSTALLFILES += $(run_singularity_INSTALL)

# capability config file
capability_config_INSTALL := $(DESTDIR)$(SYSCONFDIR)/apptainer/capability.json
$(capability_config_INSTALL):
   @echo ” INSTALL” $@
   $(V)umask 0022 && mkdir -p $(@D)
   $(V)touch $@

INSTALLFILES += $(capability_config_INSTALL)

go env GOPATH

make编译过程中用到的或者下载下来的文件在哪 go下载的临时文件都在哪里呢通常在go env GOPATH 路径下面

 ls -lha  /root/go/pkg/m
od/cache/download/github.com/total 4.0K
drwxr-xr-x 25 root root 4.0K Feb  8 02:14 .
drwxr-xr-x  7 root root   91 Feb  8 02:13 ..
drwxr-xr-x  3 root root   17 Feb  8 02:14 apex
drwxr-xr-x  5 root root   77 Feb  8 02:13 apptainer
drwxr-xr-x  3 root root   20 Feb  8 02:11 blang
drwxr-xr-x  3 root root   24 Feb  8 02:13 containerd
drwxr-xr-x  4 root root   32 Feb  8 02:11 containernetworking
drwxr-xr-x  3 root root   19 Feb  8 02:11 containers
drwxr-xr-x  3 root root   17 Feb  8 02:11 creack
drwxr-xr-x  3 root root   33 Feb  8 02:13 cyphar
drwxr-xr-x  4 root root   36 Feb  8 02:14 docker
drwxr-xr-x  3 root root   19 Feb  8 02:13 fatih
drwxr-xr-x  3 root root   17 Feb  8 02:14 go-log
drwxr-xr-x  3 root root   18 Feb  8 02:11 google
drwxr-xr-x  3 root root   18 Feb  8 02:14 gosimple
drwxr-xr-x  3 root root   27 Feb  8 02:11 hashicorp
drwxr-xr-x  8 root root  101 Feb  8 02:14 opencontainers
drwxr-xr-x  3 root root   21 Feb  8 02:11 pelletier
drwxr-xr-x  3 root root   20 Feb  8 02:11 pkg
drwxr-xr-x  3 root root   23 Feb  8 02:11 !proton!mail
drwxr-xr-x  3 root root   31 Feb  8 02:11 seccomp
drwxr-xr-x  3 root root   21 Feb  8 02:13 shopspring
drwxr-xr-x  4 root root   32 Feb  8 02:13 spf13
drwxr-xr-x  3 root root   23 Feb  8 02:13 sylabs
drwxr-xr-x  3 root root   17 Feb  8 02:13 vbauerster

make
 GO apptainer
    [+] GO_TAGS "containers_image_openpgp sylog oci_engine apptainer_engine fakeroot_engine apparmor selin
ux"go: downloading github.com/apptainer/container-key-client v0.8.0
go: downloading github.com/apptainer/sif/v2 v2.8.1
go: downloading github.com/fatih/color v1.13.0
go: downloading golang.org/x/sys v0.0.0-20220715151400-c0bba94af5f8
go: downloading github.com/apptainer/container-library-client v1.3.3
go: downloading github.com/sylabs/json-resp v0.8.1
go: downloading github.com/creack/pty v1.1.18
go: downloading github.com/opencontainers/runtime-spec v1.0.3-0.20210326190908-1c3f411f0417
go: downloading github.com/shopspring/decimal v1.3.1
go: downloading github.com/ProtonMail/go-crypto v0.0.0-20220824120805-4b6e5c587895
go: downloading gopkg.in/yaml.v2 v2.4.0
go: downloading github.com/docker/go-units v0.4.0
go: downloading golang.org/x/term v0.0.0-20210927222741-03fcf44c2211
go: downloading github.com/spf13/cobra v1.5.0
go: downloading github.com/containers/image/v5 v5.22.0
go: downloading github.com/spf13/pflag v1.0.5
go: downloading github.com/seccomp/containers-golang v0.6.0
go: downloading github.com/containerd/containerd v1.6.8
go: downloading github.com/blang/semver/v4 v4.0.0
go: downloading github.com/pkg/errors v0.9.1
go: downloading github.com/pelletier/go-toml v1.9.5
go: downloading github.com/opencontainers/runc v1.1.4
go: downloading github.com/opencontainers/go-digest v1.0.0
go: downloading github.com/opencontainers/image-spec v1.0.2-0.20211117181255-693428a734f5
go: downloading oras.land/oras-go v1.2.0
go: downloading github.com/go-log/log v0.2.0
go: downloading github.com/gosimple/slug v1.12.0
go: downloading github.com/vbauerster/mpb/v7 v7.4.2
go: downloading mvdan.cc/sh/v3 v3.5.1
go: downloading github.com/cyphar/filepath-securejoin v0.2.3
go: downloading github.com/google/uuid v1.3.0
go: downloading github.com/apex/log v1.9.0
go: downloading github.com/opencontainers/umoci v0.4.7
go: downloading github.com/docker/docker v20.10.17+incompatible
go: downloading github.com/opencontainers/selinux v1.10.1
../cmd/internal/cli/pgp.go:23:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "
https://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/sypgp/sypgp.go:35:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "https
://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/pgp.go:24:2: github.com/ProtonMail/go-crypto@v0.0.0-20220824120805-4b6e5c587895: Get "
https://proxy.golang.org/github.com/%21proton%21mail/go-crypto/@v/v0.0.0-20220824120805-4b6e5c587895.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:23:2: github.com/apex/log@v1.9.0: Get "https://proxy.golang.or
g/github.com/apex/log/@v/v1.9.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:19:2: github.com/apptainer/container-key-client@v0.8.0: Get "htt
ps://proxy.golang.org/github.com/apptainer/container-key-client/@v/v0.8.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:20:2: github.com/apptainer/container-library-client@v1.3.3: Get 
"https://proxy.golang.org/github.com/apptainer/container-library-client/@v/v1.3.3.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/sign.go:14:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/
github.com/apptainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/image/sif.go:19:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/github.com/app
tainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/siftool.go:15:2: github.com/apptainer/sif/v2@v2.8.1: Get "https://proxy.golang.org/git
hub.com/apptainer/sif/v2/@v/v2.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/plugin/module.go:23:2: github.com/blang/semver/v4@v4.0.0: Get "https://proxy.golang.org/gi
thub.com/blang/semver/v4/@v/v4.0.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:29:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:30:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:31:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:32:2: github.com/containerd/containerd@v1.6.8: Get "https://proxy.gola
ng.org/github.com/containerd/containerd/@v/v1.6.8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:22:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:23:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:38:2: github.com/containers/image/v5@v5.22.0: Get "htt
ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:39:2: github.com/containers/image/v5@v5.22.0: Get "htt
ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/conveyorPacker_oci.go:40:2: github.com/containers/image/v5@v5.22.0: Get "htt
ps://proxy.golang.org/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:24:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:25:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/oci/oci.go:26:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.o
rg/github.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/build/types/bundle.go:24:2: github.com/containers/image/v5@v5.22.0: Get "https://proxy.golang.org/g
ithub.com/containers/image/v5/@v/v5.22.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/oci/prepare_linux.go:24:2: github.com/creack/pty@v1.1.18: Get "https://prox
y.golang.org/github.com/creack/pty/@v/v1.1.18.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:19:2: github.com/cyphar/filepath-securejoin@v0.2.3: Get "https://prox
y.golang.org/github.com/cyphar/filepath-securejoin/@v/v0.2.3.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/archive/copy.go:17:2: github.com/docker/docker@v20.10.17+incompatible: Get "https://proxy.gola
ng.org/github.com/docker/docker/@v/v20.10.17+incompatible.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/archive/copy.go:18:2: github.com/docker/docker@v20.10.17+incompatible: Get "https://proxy.gola
ng.org/github.com/docker/docker/@v/v20.10.17+incompatible.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/instance_linux.go:30:2: github.com/docker/go-units@v0.4.0: Get "https://proxy.go
lang.org/github.com/docker/go-units/@v/v0.4.0.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/pgp.go:31:2: github.com/fatih/color@v1.13.0: Get "https://proxy.golang.org/github.com/
fatih/color/@v/v1.13.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/client.go:21:2: github.com/go-log/log@v0.2.0: Get "https://proxy.golang.or
g/github.com/go-log/log/@v/v0.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/crypt/crypt_dev.go:28:2: github.com/google/uuid@v1.3.0: Get "https://proxy.golang.org
/github.com/google/uuid/@v/v1.3.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/config.go:24:2: github.com/gosimple/slug@v1.12.0: Get "https://proxy.golan
g.org/github.com/gosimple/slug/@v/v1.12.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:34:2: github.com/opencontainers/go-digest@v1.0.0: Get "https://proxy.g
olang.org/github.com/opencontainers/go-digest/@v/v1.0.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/ocibundle/sif/bundle_linux.go:21:2: github.com/opencontainers/image-spec@v1.0.2-0.20211117181255-69
3428a734f5: Get "https://proxy.golang.org/github.com/opencontainers/image-spec/@v/v1.0.2-0.20211117181255-693428a734f5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:22:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:24:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:25:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/manager_linux.go:26:2: github.com/opencontainers/runc@v1.1.4: Get "https://proxy.g
olang.org/github.com/opencontainers/runc/@v/v1.1.4.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/config/oci/generate/generate.go:35:2: github.com/opencontainers/runtime-spe
c@v1.0.3-0.20210326190908-1c3f411f0417: Get "https://proxy.golang.org/github.com/opencontainers/runtime-spec/@v/v1.0.3-0.20210326190908-1c3f411f0417.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/security/selinux/selinux_supported.go:14:8: github.com/opencontainers/selinux@v1.10.1: Get
 "https://proxy.golang.org/github.com/opencontainers/selinux/@v/v1.10.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:30:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:31:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/sources/oci_unpack.go:32:2: github.com/opencontainers/umoci@v0.4.7: Get "https://pro
xy.golang.org/github.com/opencontainers/umoci/@v/v0.4.7.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/cgroups/config_linux.go:18:2: github.com/pelletier/go-toml@v1.9.5: Get "https://proxy.gola
ng.org/github.com/pelletier/go-toml/@v/v1.9.5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/bin/bin.go:22:2: github.com/pkg/errors@v0.9.1: Get "https://proxy.golang.org/github.c
om/pkg/errors/@v/v0.9.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/runtime/engine/config/oci/config.go:20:2: github.com/seccomp/containers-golang@v0.6.0: Get
 "https://proxy.golang.org/github.com/seccomp/containers-golang/@v/v0.6.0.zip": dial tcp 172.217.160.113:443: i/o timeout../cmd/internal/cli/cgroups.go:21:2: github.com/shopspring/decimal@v1.3.1: Get "https://proxy.golang.org/g
ithub.com/shopspring/decimal/@v/v1.3.1.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/cmdline/cmd.go:16:2: github.com/spf13/cobra@v1.5.0: Get "https://proxy.golang.org/github.com/spf13/
cobra/@v/v1.5.0.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/cmdline/env.go:17:2: github.com/spf13/pflag@v1.0.5: Get "https://proxy.golang.org/github.com/spf13/
pflag/@v/v1.0.5.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/endpoint/service.go:24:2: github.com/sylabs/json-resp@v0.8.1: Get "https://proxy.go
lang.org/github.com/sylabs/json-resp/@v/v0.8.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/push.go:27:2: github.com/vbauerster/mpb/v7@v7.4.2: Get "https://proxy.golang.org
/github.com/vbauerster/mpb/v7/@v/v7.4.2.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/app/apptainer/push.go:28:2: github.com/vbauerster/mpb/v7@v7.4.2: Get "https://proxy.golang.org
/github.com/vbauerster/mpb/v7/@v/v7.4.2.zip": dial tcp 172.217.160.113:443: i/o timeout../pkg/util/capabilities/process_linux.go:15:2: golang.org/x/sys@v0.0.0-20220715151400-c0bba94af5f8: Get "
https://proxy.golang.org/golang.org/x/sys/@v/v0.0.0-20220715151400-c0bba94af5f8.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/interactive/interactive.go:23:2: golang.org/x/term@v0.0.0-20210927222741-03fcf44c2211
: Get "https://proxy.golang.org/golang.org/x/term/@v/v0.0.0-20210927222741-03fcf44c2211.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/remote.go:27:2: gopkg.in/yaml.v2@v2.4.0: Get "https://proxy.golang.org/gopkg.in/yam
l.v2/@v/v2.4.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/util/shell/interpreter/interpreter.go:25:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.gola
ng.org/mvdan.cc/sh/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:20:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.golang.org/mvdan.cc/s
h/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/build/files/files.go:21:2: mvdan.cc/sh/v3@v3.5.1: Get "https://proxy.golang.org/mvdan.cc/s
h/v3/@v/v3.5.1.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/credential/login_handler.go:20:2: oras.land/oras-go@v1.2.0: Get "https://proxy.gola
ng.org/oras.land/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/remote/credential/login_handler.go:26:2: oras.land/oras-go@v1.2.0: Get "https://proxy.gola
ng.org/oras.land/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:37:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:38:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:39:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeout../internal/pkg/client/oras/oras.go:40:2: oras.land/oras-go@v1.2.0: Get "https://proxy.golang.org/oras.lan
d/oras-go/@v/v1.2.0.zip": dial tcp 172.217.160.113:443: i/o timeoutmake: *** [apptainer] Error 1

看起来是编译过程中网络连接失败，造成部分库下载不到，导致编译失败。可以尝试如下方法解决问题：

检查网络连接是否正常，如果有问题请尝试修复。

重试编译，因为有时网络问题是暂时的，重试可能就可以解决问题。

手动下载所需库并放入本地目录，可以避免编译过程中从网络上下载，保证编译成功。

编译过程中产生的中间文件通常在编译命令执行的当前目录下的中间目录，具体目录名称和编译工具有关。

另外，提供一些关于编译失败的通用解决方案：

检查代码是否有语法错误，修复错误后重试编译。

检查所需的环境变量和依赖是否已经配置，确保环境正确配置。

清理编译过程中产生的缓存文件，重新编译。

查阅相关文档，以了解编译要求和建议的解决方案。

sudo yum install如何安装本地存在的文件

如果您有一个本地存在的 RPM 包，您可以使用以下命令安装它：

sudo yum localinstall <filename>.rpm

non-setuid和setuid是关于Unix系统文件权限的术语。

当一个程序被标记为setuid时，当它被执行时，它的权限将从它的所有者变为它的执行者。这意味着即使普通用户执行了一个以setuid标记的程序，该程序仍将具有更高的权限，以便完成某些任务。

相反，当一个程序被标记为non-setuid时，该程序仅具有它的所有者的权限，即使它被普通用户执行。

因此，在上面的代码中，sudo yum install -y apptainer将安装一个没有setuid标记的版本，而sudo yum install -y apptainer-suid将安装一个以setuid标记的版本。

通常，在安全方面，使用non-setuid版本更安全，因为它仅允许该程序以其所有者的权限运行，而不允许它以执行者的权限运行。然而，如果程序需要更高的权限才能完成任务，则必须使用setuid版本。

sudo yum install -y apptainer这段代码是在执行在Red Hat系列的操作系统（如CentOS、Fedora等）上的软件包安装。

yum是一个在Red Hat系列操作系统上进行软件包管理的工具。它允许安装、升级和删除软件包。

在这个代码中，sudo命令用于在管理员权限下执行命令。yum install -y命令是安装软件包的命令，其中-y选项用于默认回答“是”，以便在没有用户交互的情况下安装软件包。最后，apptainer是要安装的软件包的名称。

安装的软件包将被下载并存储在操作系统的软件仓库中，通常在/var/cache/yum或/var/lib/yum目录下。安装后的文件将安装在系统的文件系统中，通常在/usr/目录下。

Install RPM from EPEL or Fedora
Multiple architectures of RPMs are available for Red Hat Enterprise Linux and Fedora.

First, on Red Hat Enterprise Linux derived systems enable the EPEL repositories like this:

$ sudo yum install -y epel-release
Then to install a non-setuid installation of Apptainer do:

$ sudo yum install -y apptainer
or for a setuid installation do:

$ sudo yum install -y apptainer-suid
Install from GitHub release RPMs
Alternatively, x86_64 RPMs are available on GitHub immediately after each Apptainer release and they can be installed directly from there. For the non-setuid installation:

$ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.5/apptainer-1.1.5-1.x86_64.rpm
For the setuid installation do above command first and then this one:

$ sudo yum install -y https://github.com/apptainer/apptainer/releases/download/v1.1.5/apptainer-suid-1.1.5-1.x86_64.rpm

singularity 安装与使用 – 简书成功！！

echo ‘export PATH=~/.aspera/connect/bin/:$PATH’ >> ~/.bashrc
source ~/.bashrc singularity/INSTALL.md at master · apptainer/singularity · GitHub

如何直接使用sigularity 或者apptainer调用软件 virsorter2

Option 3

If you have apptainer (formerly known as singularity) installed (typical in HPC clusters), the following is the most convenient. Also use the option if you have issues with conda.
apptainer build virsorter2.sif docker://jiarong/virsorter:latest
You will get a file virsorter2.sif, which is a singularity image that can be run like a binary executable file. You can use the absolute path of this file to replace virsorter in commands for the rest of the tutorial. Also this image has the database and dependencies included, so you can skip the Download database and dependencies stephttps://github.com/jiarong/VirSorter2#download-database-and-dependencies below.

singularity使用

singularity build metawrap.sif docker://lmwbio/metawrap_1.3.2_binning_fastq_gz


INFO:    Starting build...
Getting image source signatures

sourmash 先安装pip 再用pip安装sourmashGitHub – sourmash-bio/sourmash: Quickly search, compare, and analyze genomic and metagenomic data sets.

Singularity 可以直接从 Docker Hub 下载镜像，您可以使用以下命令：

singularity pull docker://<DOCKER_IMAGE_NAME>:<TAG>

问题1. Singularity 可以直接从 Docker Hub 下载镜像速度太慢，我应该怎么办问题2. 我可以先把docker镜像下载到本地，然后使用singularity来安装本地的镜像吗？具体应该怎么做

如果 Singularity 从 Docker Hub 下载镜像速度太慢，您可以尝试以下几种方法：
- 使用私有镜像仓库，如 Google Container Registry，Amazon Elastic Container Registry，或 Quay.io。
- 使用更快的网络，例如 VPN 或私有网络。
- 使用国内的 Docker 镜像仓库，例如 Docker 中国镜像。
是的，您可以先下载 Docker 镜像到本地，然后使用 Singularity 安装本地的镜像。

具体操作如下：

使用 docker save 命令将镜像存储到本地：

docker save <IMAGE_NAME>:<TAG> -o <SAVE_FILE>.tar

docker save ubuntu:20.04 -o ubuntu_20.04.tar

使用 singularity image.create 命令将存储文件转换为 Singularity 容器：

singularity image.create <SINGULARITY_CONTAINER>.sif

例如：

singularity image.create ubuntu_20.04.sif

使用 singularity import 命令从存储文件导入镜像：

singularity import <SINGULARITY_CONTAINER>.sif <SAVE_FILE>.tar

singularity import ubuntu_20.04.sif ubuntu_20.04.tar

现在，您应该已经有了一个本地的 Singularity 容器，可以快速启动和运行。

windows 系统安装dockerInstall on Windows | Docker Documentation

在 Windows 系统中，可以使用 Docker Desktop 软件下载 Docker 镜像。

首先，请确保已安装 Docker Desktop，并已启动 Docker 引擎。

然后，打开命令提示符或 PowerShell，输入以下命令：

docker pull lmwbio/metawrap_1.3.2_binning_fastq_gz

这将下载镜像到您的计算机上，并将其存储在 Docker 镜像库中。

稍后，您可以使用 docker run 命令启动该镜像。

例如：

docker run lmwbio/metawrap_1.3.2_binning_fastq_gz

metaphlan2

https://anaconda.org/bioconda/metaphlan2

GitHub – biobakery/MetaPhlAn2

metawrap

最终通过把metawrap下载到本地然后使用conda安装本地软件

conda install --use-local *****

GitHub – bxlab/metaWRAP: MetaWRAP – a flexible pipeline for genome-resolved metagenomic data analysis

container/Singularity.metawrap at master · hexmek/container · GitHub

在 CentOS 系统中安装 metaWRAP 使用 Singularity 可以通过以下步骤进行：

安装 Singularity：
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sudo yum install singularity

创建一个 Singularity 容器文件，其内容如下：
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Bootstrap: docker From: ubuntu:16.04 %post apt-get update apt-get -y install wget wget https://github.com/bzhangHu/metaWRAP/releases/download/v1.0/metaWRAP-Linux.tar.gz tar -xvzf metaWRAP-Linux.tar.gz rm metaWRAP-Linux.tar.gz

创建 Singularity 容器：
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sudo singularity build metawrap.sif metawrap.def

运行容器：

singularity run metawrap.sif

这样，您就可以在 Singularity 容器中使用 metaWRAP 了。