Hello,
I am trying to create a virtual env via conda with a provided .yml script ,for testing a tool. Here the yml:
#slinker.yml
name: slinker
channels:
- anaconda
- conda-forge
- bioconda
- defaults
dependencies:
- pandas
- plotly
- pybedtools
- pysam
When trying with conda env create ,I get the following errors:
UnsatisfiableError: The following specifications were found to be incompatible with each other:
Output in format: Requested package -> Available versions
Package pysam conflicts for:
pybedtools==0.8.1 -> pysam[version='>=0.16|>=0.8.1']
pysam==0.15.4
Package pypy3.9 conflicts for:
pandas -> pypy3.9[version='>=7.3.9']
pandas -> numpy[version='>=1.19.2,<2.0a0'] -> pypy3.9[version='7.3.*|7.3.8.*|7.3.9.*|>=7.3.8']
etc.. for many packages dependencies and conflicts.
Finally:
The following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.17=0
- feature:|@/linux-64::__glibc==2.17=0
- pandas -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
- pybedtools==0.8.1 -> libgcc-ng[version='>=7.5.0'] -> __glibc[version='>=2.17']
Now , I try again same creation with mamba :
mamba env create --file env/slinker.yml --prefix=./Slinker_env
Errors appear:
Updating specs:
- pandas
- plotly
- pybedtools
- pysam
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/bzip2-1.0.8-h7b6447c_0'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/c-ares-1.18.1-h7f8727e_0'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/libedit-3.1.20210910-h7f8727e_0'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/libev-4.33-h7f8727e_1'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/libffi-3.3-he6710b0_2'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/ncurses-6.3-h7f8727e_2'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/pip-21.2.4-py39h06a4308_0'
ERROR Caught a filesystem error: Permission denied: '/shared/ifbstor1/software/miniconda/pkgs/wheel-0.37.1-pyhd3eb1b0_0'
After trying to download packages :
Install:
───────────────────────────────────────────────────────────────────────────────────
_libgcc_mutex 0.1 conda_forge conda-forge/linux-64 Cached
_openmp_mutex 4.5 2_gnu conda-forge/linux-64 Cached
bedtools 2.30.0 h468198e_3 bioconda/linux-64 Cached
blas 1.0 openblas anaconda/linux-64 48 KB
bottleneck 1.3.4 py39hce1f21e_0 anaconda/linux-64 139 KB
bzip2 1.0.8 h7b6447c_0 anaconda/linux-64 105 KB
c-ares 1.18.1 h7f8727e_0 anaconda/linux-64 119 KB
ca-certificates 2022.4.26 h06a4308_0 anaconda/linux-64 132 KB
certifi 2022.6.15 py39h06a4308_0 anaconda/linux-64 156 KB
keyutils 1.6.1 h166bdaf_0 conda-forge/linux-64 Cached
krb5 1.19.3 h3790be6_0 conda-forge/linux-64 Cached
ld_impl_linux-64 2.38 h1181459_1 anaconda/linux-64 732 KB
libcurl 7.83.1 h7bff187_0 conda-forge/linux-64 Cached
libdeflate 1.10 h7f98852_0 conda-forge/linux-64 Cached
libedit 3.1.20210910 h7f8727e_0 anaconda/linux-64 191 KB
libev 4.33 h7f8727e_1 anaconda/linux-64 106 KB
libffi 3.3 he6710b0_2 anaconda/linux-64 54 KB
libgcc-ng 12.1.0 h8d9b700_16 conda-forge/linux-64 Cached
libgfortran-ng 11.2.0 h00389a5_1 anaconda/linux-64 19 KB
libgfortran5 11.2.0 h1234567_1 anaconda/linux-64 5 MB
libgomp 12.1.0 h8d9b700_16 conda-forge/linux-64 Cached
libnghttp2 1.47.0 h727a467_0 conda-forge/linux-64 Cached
libopenblas 0.3.20 h043d6bf_1 anaconda/linux-64 10 MB
libssh2 1.10.0 h8f2d780_0 anaconda/linux-64 304 KB
libstdcxx-ng 11.2.0 h1234567_1 anaconda/linux-64 6 MB
libzlib 1.2.12 h166bdaf_1 conda-forge/linux-64 Cached
ncurses 6.3 h7f8727e_2 anaconda/linux-64 1 MB
numexpr 2.8.1 py39hd2a5715_2 anaconda/linux-64 130 KB
numpy 1.22.3 py39h7a5d4dd_0 anaconda/linux-64 10 KB
numpy-base 1.22.3 py39hb8be1f0_0 anaconda/linux-64 7 MB
openssl 1.1.1o h7f8727e_0 anaconda/linux-64 4 MB
packaging 21.3 pyhd3eb1b0_0 anaconda/noarch 35 KB
pandas 1.4.2 py39h295c915_0 anaconda/linux-64 13 MB
pip 21.2.4 py39h06a4308_0 anaconda/linux-64 2 MB
plotly 5.6.0 pyhd3eb1b0_0 anaconda/noarch 7 MB
pybedtools 0.9.0 py39h6935b12_1 bioconda/linux-64 12 MB
pyparsing 3.0.4 pyhd3eb1b0_0 anaconda/noarch 78 KB
pysam 0.19.1 py39h5030a8b_0 bioconda/linux-64 3 MB
python 3.9.12 h12debd9_1 anaconda/linux-64 23 MB
python-dateutil 2.8.2 pyhd3eb1b0_0 anaconda/noarch 241 KB
python_abi 3.9 2_cp39 conda-forge/linux-64 Cached
pytz 2022.1 py39h06a4308_0 anaconda/linux-64 259 KB
readline 8.1.2 h7f8727e_1 anaconda/linux-64 423 KB
setuptools 61.2.0 py39h06a4308_0 anaconda/linux-64 1 MB
six 1.16.0 pyhd3eb1b0_1 anaconda/noarch 19 KB
sqlite 3.38.5 hc218d9a_0 anaconda/linux-64 1 MB
tenacity 8.0.1 py39h06a4308_0 anaconda/linux-64 34 KB
tk 8.6.12 h1ccaba5_0 anaconda/linux-64 3 MB
tzdata 2022a hda174b7_0 anaconda/noarch 121 KB
wheel 0.37.1 pyhd3eb1b0_0 anaconda/noarch 31 KB
xz 5.2.5 h7f8727e_1 anaconda/linux-64 389 KB
zlib 1.2.12 h166bdaf_1 conda-forge/linux-64 Cached
Summary:
Install: 52 packages
Total download: 102 MB
InvalidArchiveError("Error with archive /shared/home/mkondili/.conda/pkgs/pybedtools-0.9.0-py39h6935b12_1.tar.bz2. You probably need to delete and re-download or re-create this file. Message from libarchive was:\n\nCan't create 'lib/python3.9/site-packages/pybedtools/test/data/a.bed.gz'")
InvalidArchiveError("Error with archive /shared/home/mkondili/.conda/pkgs/pytz-2022.1-py39h06a4308_0.tar.bz2. You probably need to delete and re-download or re-create this file. Message from libarchive was:\n\nCan't create 'lib/python3.9/site-packages/pytz/zoneinfo/Pacific/Midway'")
InvalidArchiveError("Error with archive /shared/home/mkondili/.conda/pkgs/libopenblas-0.3.20-h043d6bf_1.tar.bz2. You probably need to delete and re-download or re-create this file. Message from libarchive was:\n\nFailed to create dir 'info/licenses'")
&
[Errno 122] Disk quota exceeded: '/shared/home/mkondili/.conda/pkgs/pip-21.2.4-py39h06a4308_0.tar.bz2 , similar message for other packages, that I finally deleted from .conda/pkgs
Could anyone help me find the dependencies and instruct me how to install them locally, and create the environment please ?