Closed wietse1 closed 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
...
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The following packages will be SUPERSEDED by a higher-priority channel: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 <<<<<<<<<<<<<<<<<<<<<<
$ /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=
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