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xiezhq / ISEScan

A python pipeline to identify IS (Insertion Sequence) elements in genome and metagenome
Apache License 2.0
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can not install using bioconda #34

Closed wietse1 closed 3 years ago

wietse1 commented 3 years ago

dear,

i tried following the steps for bioconda install in a terminal using fedora 29

i receiver nex error when try the install command for ISEscan:

(base) [guest@desktop-bdo3m4f ~]$ conda install isescan Collecting package metadata (current_repodata.json): done Solving environment: done

Package Plan

environment location: /home/guest/miniconda3

added / updated specs:

The following NEW packages will be INSTALLED:

biopython conda-forge/linux-64::biopython-1.78-py38h25fe258_1 blast bioconda/linux-64::blast-2.5.0-hc0b0e79_3 boost conda-forge/linux-64::boost-1.72.0-py38h1e42940_1 boost-cpp conda-forge/linux-64::boost-cpp-1.72.0-h8e57a91_0 bzip2 conda-forge/linux-64::bzip2-1.0.8-h516909a_3 fastcluster conda-forge/linux-64::fastcluster-1.1.26-py38hc5bc63f_2 fraggenescan bioconda/linux-64::fraggenescan-1.30-h470a237_2 hmmer bioconda/linux-64::hmmer-3.3.2-he1b5a44_0 icu conda-forge/linux-64::icu-64.2-he1b5a44_1 isescan bioconda/linux-64::isescan-1.7.2.1-h516909a_0 libblas conda-forge/linux-64::libblas-3.9.0-8_openblas libcblas conda-forge/linux-64::libcblas-3.9.0-8_openblas libgfortran-ng conda-forge/linux-64::libgfortran-ng-7.5.0-h14aa051_18 libgfortran4 conda-forge/linux-64::libgfortran4-7.5.0-h14aa051_18 liblapack conda-forge/linux-64::liblapack-3.9.0-8_openblas libopenblas conda-forge/linux-64::libopenblas-0.3.12-pthreads_hb3c22a3_1 numpy conda-forge/linux-64::numpy-1.18.1-py38h8854b6b_1 perl conda-forge/linux-64::perl-5.32.0-h36c2ea0_0 python_abi conda-forge/linux-64::python_abi-3.8-1_cp38 scipy conda-forge/linux-64::scipy-1.5.3-py38h828c644_0

The following packages will be UPDATED:

ca-certificates pkgs/main::ca-certificates-2020.10.14~ --> conda-forge::ca-certificates-2020.12.5-ha878542_0 certifi pkgs/main/noarch::certifi-2020.6.20-p~ --> conda-forge/linux-64::certifi-2020.12.5-py38h578d9bd_1 openssl 1.1.1h-h7b6447c_0 --> 1.1.1j-h27cfd23_0

The following packages will be SUPERSEDED by a higher-priority channel:

conda pkgs/main::conda-4.9.2-py38h06a4308_0 --> conda-forge::conda-4.9.2-py38h578d9bd_0

Proceed ([y]/n)? y

Preparing transaction: failed

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

Traceback (most recent call last):
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/exceptions.py", line 1079, in __call__
    return func(*args, **kwargs)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/cli/main.py", line 84, in _main
    exit_code = do_call(args, p)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/cli/conda_argparse.py", line 83, in do_call
    return getattr(module, func_name)(args, parser)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/cli/main_install.py", line 20, in execute
    install(args, parser, 'install')
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 317, in install
    handle_txn(unlink_link_transaction, prefix, args, newenv)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/cli/install.py", line 346, in handle_txn
    unlink_link_transaction.execute()
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 244, in execute
    self.verify()
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/common/io.py", line 88, in decorated
    return f(*args, **kwds)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 221, in verify
    self.prepare()
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 210, in prepare
    grps = self._prepare(self.transaction_context, stp.target_prefix,
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 287, in _prepare
    packages_info_to_link = tuple(read_package_info(prec, pcrec)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/core/link.py", line 287, in <genexpr>
    packages_info_to_link = tuple(read_package_info(prec, pcrec)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/gateways/disk/read.py", line 90, in read_package_info
    paths_data = read_paths_json(epd)
  File "/home/guest/miniconda3/lib/python3.8/site-packages/conda/gateways/disk/read.py", line 160, in read_paths_json
    data = json.load(paths_json)
  File "/home/guest/miniconda3/lib/python3.8/json/__init__.py", line 293, in load
    return loads(fp.read(),
  File "/home/guest/miniconda3/lib/python3.8/json/__init__.py", line 357, in loads
    return _default_decoder.decode(s)
  File "/home/guest/miniconda3/lib/python3.8/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/guest/miniconda3/lib/python3.8/json/decoder.py", line 355, in raw_decode
    raise JSONDecodeError("Expecting value", s, err.value) from None
json.decoder.JSONDecodeError: Expecting value: line 1 column 1 (char 0)

$ /home/guest/miniconda3/bin/conda install isescan

environment variables: CIO_TEST= CONDA_DEFAULT_ENV=base CONDA_EXE=/home/guest/miniconda3/bin/conda CONDA_PREFIX=/home/guest/miniconda3 CONDA_PROMPT_MODIFIER=(base) CONDA_PYTHON_EXE=/home/guest/miniconda3/bin/python CONDA_ROOT=/home/guest/miniconda3 CONDA_SHLVL=1 CURL_CA_BUNDLE= MODULEPATH=/etc/scl/modulefiles:/etc/scl/modulefiles:/usr/share/Modules/modulefil es:/etc/modulefiles:/usr/share/modulefiles PATH=/home/guest/miniconda3/bin:/home/guest/.local/bin:/home/guest/bin:/hom e/guest/.local/bin:/home/guest/bin:/home/guest/miniconda3/bin:/home/gu est/miniconda3/condabin:/home/guest/.local/bin:/home/guest/bin:/usr/sh are/Modules/bin:/usr/local/bin:/usr/local/sbin:/usr/bin:/usr/sbin REQUESTS_CA_BUNDLE= SSL_CERT_FILE=

 active environment : base
active env location : /home/guest/miniconda3
        shell level : 1
   user config file : /home/guest/.condarc

populated config files : /home/guest/.condarc conda version : 4.9.2 conda-build version : not installed python version : 3.8.5.final.0 virtual packages : glibc=2.28=0 unix=0=0 __archspec=1=x86_64 base environment : /home/guest/miniconda3 (writable) channel URLs : https://conda.anaconda.org/conda-forge/linux-64 https://conda.anaconda.org/conda-forge/noarch https://conda.anaconda.org/bioconda/linux-64 https://conda.anaconda.org/bioconda/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 : /home/guest/miniconda3/pkgs /home/guest/.conda/pkgs envs directories : /home/guest/miniconda3/envs /home/guest/.conda/envs platform : linux-64 user-agent : conda/4.9.2 requests/2.24.0 CPython/3.8.5 Linux/5.0.10-200.fc29.x86_64 fedora/29 glibc/2.28 UID:GID : 1000:1000 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?

regards

xiezhq commented 3 years ago

It seems not the ISEScan specific issue. Did you strictly follow the instructions on https://github.com/xiezhq/ISEScan#Bioconda-install? I just followed those install instructions, everything was going well and ISEScan was installed without any issue:

(base) [xiezhq@localhost ~]$ which isescan.py
~/miniconda3/bin/isescan.py
(base) [xiezhq@localhost ~]$ ~/miniconda3/bin/isescan.py -h
usage: isescan [-h] [--version] [--removeShortIS] [--no-FragGeneScan] [--nthread NTHREAD]
               seqfile path2proteome path2hmm
...