Skip to content
Snippets Groups Projects
Commit a7d50eeb authored by Helene Rimbert's avatar Helene Rimbert
Browse files

Delete README-hpc2.md

parent 7c1bb318
No related branches found
No related tags found
No related merge requests found
# Utilisation sur HPC2 (Cluster du mesocentre)
Un environnement conda a été créé pour les dépendances du pipeline.
Pour charger ces dépendances:
```console
$ module load gcc/8.1.0 python/3.7.1 snakemake/5.6.0 ncbi-blast/2.2.30+ gmap/20200408
$ conda activate transfertAnnot
```
Rappel des dépendances:
* snakemake >=5.6 (via les modules)
* blast+ >=2.2 (via les modules)
* gmap >= 2020 (via les modules)
* bedtools >=2.27
* blat >=36
* biopython >=1.70
* exonerate >=2.4
* genometools >=1.5
* gffread >=0.11
* numpy >=1.12
* pandas >=0.23
* pysam >=0.15
* python >=3..5
* samtools >=1.9
```console
$ conda list
# packages in environment at /storage/groups/gdec/bin/tools/miniconda/miniconda2/envs/transfertAnnot:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
bcftools 1.9 h47928c2_2 bioconda
bedtools 2.27.1 he860b03_3 bioconda
biopython 1.70 np112py35_1 bioconda
blas 1.0 mkl
blat 36 0 bioconda
bzip2 1.0.8 h7b6447c_0
ca-certificates 2020.1.1 0
certifi 2018.8.24 py35_1
curl 7.61.0 h84994c4_0
exonerate 2.4.0 haf93ef1_3 bioconda
freetype 2.9.1 h8a8886c_1
genometools-genometools 1.5.10 h470a237_1 bioconda
gettext 0.19.8.1 hd7bead4_3
gffread 0.11.7 h8b12597_0 bioconda
glib 2.63.1 h5a9c865_0
htslib 1.9 h4da6232_3 bioconda
intel-openmp 2019.4 243
jpeg 9b h024ee3a_2
libcurl 7.61.0 h1ad7b7a_0
libdeflate 1.0 h14c3975_1 bioconda
libedit 3.1.20181209 hc058e9b_0
libffi 3.2.1 hd88cf55_4
libgcc-ng 9.1.0 hdf63c60_0
libgfortran-ng 7.3.0 hdf63c60_0
libpng 1.6.37 hbc83047_0
libssh2 1.8.0 h9cfc8f7_4
libstdcxx-ng 9.1.0 hdf63c60_0
libtiff 4.1.0 h2733197_1
lz4-c 1.9.2 he6710b0_0
mkl 2018.0.3 1
mmtf-python 1.0.2 py35_0 bioconda
msgpack-python 0.5.6 py35h6bb024c_1
ncurses 6.1 he6710b0_1
numpy 1.12.1 py35hca0bb5e_1
olefile 0.46 py35_0
openssl 1.0.2u h7b6447c_0
pandas 0.23.4 py35h04863e7_0
pcre 8.43 he6710b0_0
pillow 5.2.0 py35heded4f4_0
pip 10.0.1 py35_0
pysam 0.15.2 py35h0380709_0 bioconda
python 3.5.6 hc3d631a_0
python-dateutil 2.8.1 py_0
pytz 2020.1 py_0
readline 7.0 h7b6447c_5
reportlab 3.5.6 py35he686d34_0
samtools 1.9 h10a08f8_12 bioconda
setuptools 40.2.0 py35_0
six 1.15.0 py_0
sqlite 3.31.1 h7b6447c_0
tk 8.6.8 hbc83047_0
wheel 0.31.1 py35_0
xz 5.2.5 h7b6447c_0
zlib 1.2.11 h7b6447c_3
zstd 1.4.4 h0b5b093_3
```
On peut ensuite cloner le dépot et utiliser le pipeline.
\ No newline at end of file
0% Loading or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment