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README-hpc2.md

+# 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.
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