2022-11-08_AS实践1 leafcutter-安装1

作者: jiarf | 来源:发表于2022-11-08 17:11 被阅读0次

conda create -n leafcutter python=2.7
conda activate leafcutter
samtools 
regtools
conda install -c bioconda regtools

regtools install

清华镜像源怀疑有问题，所以重新加了豆瓣的镜像源，但是安装包还是不行
先删除所有的镜像

conda config --remove-key channels

添加镜像

conda config --add channels https://pypi.douban.com/anaconda/cloud/conda-forge/
conda config --add channels https://pypi.douban.com/anaconda/cloud/msys2/
conda config --add channels https://pypi.douban.com/anaconda/cloud/bioconda/
conda config --add channels https://pypi.douban.com/anaconda/cloud/menpo/
conda config --add channels https://pypi.douban.com/anaconda/cloud/pytorch/

显示源

conda config --set show_channel_urls yes

显示目前的镜像

conda config --show-sources

查看

(leafcutter)... data1/jiarongf/specise_compare_HGPS/AS
$
history conda config --set ssl_verify TRUE
-bash: history: conda: numeric argument required
(leafcutter) .../data1/jiarongf/specise_compare_HGPS/AS
$
conda config --set ssl_verify TRUE
(leafcutter) .../data1/jiarongf/specise_compare_HGPS/AS
$
conda config --show-sources
==> /home/jiarongf/.condarc <==
envs_dirs:
  - /data1/jiarongf/anaconda3/envs
  - ~/my-envs
ssl_verify: True
channels:
  - https://pypi.douban.com/anaconda/cloud/bioconda/
  - https://pypi.douban.com/anaconda/cloud/pytorch/
  - https://pypi.douban.com/anaconda/cloud/menpo/
  - https://pypi.douban.com/anaconda/cloud/msys2/
  - https://pypi.douban.com/anaconda/cloud/conda-forge/
  - defaults
show_channel_urls: True

还是没有安装成功，
报错原因

Collecting package metadata (current_repodata.json): ...working... failed

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

    Traceback (most recent call last):
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1125, in __call__
        return func(*args, **kwargs)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/main.py", line 86, in main_subshell
        exit_code = do_call(args, p)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 93, in do_call
        return getattr(module, func_name)(args, parser)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/notices/core.py", line 72, in wrapper
        return_value = func(*args, **kwargs)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 22, in execute
        install(args, parser, 'install')
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/cli/install.py", line 256, in install
        unlink_link_transaction = solver.solve_for_transaction(
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 152, in solve_for_transaction
        unlink_precs, link_precs = self.solve_for_diff(update_modifier, deps_modifier,
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 195, in solve_for_diff
        final_precs = self.solve_final_state(update_modifier, deps_modifier, prune, ignore_pinned,
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 300, in solve_final_state
        ssc = self._collect_all_metadata(ssc)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/common/io.py", line 86, in decorated
        return f(*args, **kwds)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 463, in _collect_all_metadata
        index, r = self._prepare(prepared_specs)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/solve.py", line 1057, in _prepare
        reduced_index = get_reduced_index(self.prefix, self.channels,
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/index.py", line 297, in get_reduced_index
        new_records = SubdirData.query_all(spec, channels=channels, subdirs=subdirs,
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 152, in query_all
        result = tuple(concat(executor.map(subdir_query, channel_urls)))
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 611, in result_iterator
        yield fs.pop().result()
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 439, in result
        return self.__get_result()
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/_base.py", line 388, in __get_result
        raise self._exception
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/concurrent/futures/thread.py", line 57, in run
        result = self.fn(*self.args, **self.kwargs)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 144, in <lambda>
        subdir_query = lambda url: tuple(SubdirData(Channel(url), repodata_fn=repodata_fn).query(
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 157, in query
        self.load()
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 222, in load
        _internal_state = self._load()
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 419, in _load
        _internal_state = self._process_raw_repodata_str(raw_repodata_str)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/site-packages/conda/core/subdir_data.py", line 492, in _process_raw_repodata_str
        json_obj = json.loads(raw_repodata_str or '{}')
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/__init__.py", line 357, in loads
        return _default_decoder.decode(s)
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/decoder.py", line 337, in decode
        obj, end = self.raw_decode(s, idx=_w(s, 0).end())
      File "/data1/jiarongf/anaconda_se/anaconda3/lib/python3.8/json/decoder.py", line 353, in raw_decode
        obj, end = self.scan_once(s, idx)
    json.decoder.JSONDecodeError: Expecting property name enclosed in double quotes: line 1 column 98 (char 97)

`$ /data1/jiarongf/anaconda_se/anaconda3/bin/conda install -c bioconda regtools`

  environment variables:
                 CIO_TEST=<not set>
        CONDA_DEFAULT_ENV=leafcutter
                CONDA_EXE=/data1/jiarongf/anaconda_se/anaconda3/bin/conda
             CONDA_PREFIX=/data1/jiarongf/anaconda3/envs/leafcutter
           CONDA_PREFIX_1=/data1/jiarongf/anaconda_se/anaconda3
    CONDA_PROMPT_MODIFIER=(leafcutter)
         CONDA_PYTHON_EXE=/data1/jiarongf/anaconda_se/anaconda3/bin/python
               CONDA_ROOT=/data1/jiarongf/anaconda_se/anaconda3
              CONDA_SHLVL=2
           CURL_CA_BUNDLE=<not set>
                  MANPATH=/data1/jiarongf/learning/cancer-
                          WES/run/gnuplot-5.4.3/gnuplot/share/man/man1:
                     PATH=/data1/jiarongf/anaconda_se/anaconda3/bin:/home/jiarongf/.local/bin:/d
                          ata1/jiarongf/software/TrimGalore-0.6.6:/data1/jiarongf/HGPS_Hic_seq/h
                          ic-pro/HiC-Pro-3.1.0/bin:/home/jiarongf/.aspera/connect/bin:/data1/jia
                          rongf/anaconda3/envs/KG/lib/nltk_data-gh-
                          pages/nltk_data:/data1/jiarongf/learning/cancer-WES/run/gatk-4.2.6.1:/
                          data1/jiarongf/other:/data1/jiarongf/learning/cancer-
                          WES/run/gnuplot-5.4.3/gnuplot/bin:/data1/jiarongf/learning/cancer-WES/
                          run:/data1/tongxin/software/annovar:/data1/jiarongf/anaconda_se/anacon
                          da3/bin/python:/data1/jiarongf/software:/data1/jiarongf/software/ncbi-
                          blast/bin:/data1/jiarongf/software/sratoolkit.2.11.0-centos_linux64/bi
                          n:/data1/nyy/HGPS_scRNAseq/cellranger-6.0.1:/data1/jiarongf/RNA_seq/tr
                          anscript/data/RNAseq/RNAseq/subread-1.6.0-Linux-x86_64/bin:/data1/jiar
                          ongf/RNA_seq/transcript/fastp:/data1/jiarongf/Knowledge_Graph/metamap/
                          metamap_bag/bag/public_mm/bin:/data1/jiarongf/software/jdl/jdk-11.0.10
                          /bin:/home/jiarongf/.conda/envs/jupyter_notebook/lib/python3.6/site-pa
                          ckages:/data1/neo4j/neo4j-community-4.2.1/bin:/data/yangpp/Space_Range
                          r/spaceranger-1.2.0:/data1/jiarongf/anaconda3/envs/leafcutter/bin:/dat
                          a1/jiarongf/anaconda_se/anaconda3:/data1/jiarongf/anaconda_se/anaconda
                          3/bin:/data1/jiarongf/anaconda_se/anaconda3/condabin:/data/anaconda3/b
                          in:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/g
                          ames:/usr/local/games:/snap/bin
          PKG_CONFIG_PATH=/data1/jiarongf/anaconda3/lib/pkgconfig
                 REF_PATH=$/data1/jiarongf/learning/cancer-
                          WES/5.GATK/ref/cache/%2s/%2s/%s:http://www.ebi.ac.uk/ena/cram/md5/%s
       REQUESTS_CA_BUNDLE=<not set>
            SSL_CERT_FILE=<not set>

     active environment : leafcutter
    active env location : /data1/jiarongf/anaconda3/envs/leafcutter
            shell level : 2
       user config file : /home/jiarongf/.condarc
 populated config files : /home/jiarongf/.condarc
          conda version : 4.14.0
    conda-build version : 3.21.4
         python version : 3.8.8.final.0
       virtual packages : __linux=5.4.0=0
                          __glibc=2.27=0
                          __unix=0=0
                          __archspec=1=x86_64
       base environment : /data1/jiarongf/anaconda_se/anaconda3  (writable)
      conda av data dir : /data1/jiarongf/anaconda_se/anaconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://conda.anaconda.org/bioconda/linux-64
                          https://conda.anaconda.org/bioconda/noarch
                          http://mirrors.ustc.edu.cn/anaconda/pkgs/free/linux-64
                          http://mirrors.ustc.edu.cn/anaconda/pkgs/free/noarch
                          http://pypi.douban.com/anaconda/cloud/bioconda/linux-64
                          http://pypi.douban.com/anaconda/cloud/bioconda/noarch
                          http://pypi.douban.com/anaconda/cloud/pytorch/linux-64
                          http://pypi.douban.com/anaconda/cloud/pytorch/noarch
                          http://pypi.douban.com/anaconda/cloud/menpo/linux-64
                          http://pypi.douban.com/anaconda/cloud/menpo/noarch
                          http://pypi.douban.com/anaconda/cloud/msys2/linux-64
                          http://pypi.douban.com/anaconda/cloud/msys2/noarch
                          http://pypi.douban.com/anaconda/cloud/conda-forge/linux-64
                          http://pypi.douban.com/anaconda/cloud/conda-forge/noarch
          package cache : /data1/jiarongf/anaconda_se/anaconda3/pkgs
                          /home/jiarongf/.conda/pkgs
       envs directories : /data1/jiarongf/anaconda3/envs
                          /home/jiarongf/my-envs
                          /data1/jiarongf/anaconda_se/anaconda3/envs
                          /home/jiarongf/.conda/envs
               platform : linux-64
             user-agent : conda/4.14.0 requests/2.25.1 CPython/3.8.8 Linux/5.4.0-110-generic ubuntu/18.04.6 glibc/2.27
                UID:GID : 1005:1005
             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.
Would you like conda to send this report to the core maintainers?

[y/N]: 
Timeout reached. No report sent.

没有解决，
用gitclone安装

2022-11-08_AS实践1 leafcutter-安装1

regtools install

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