Requirements for some workflows.

PRO-seq/PRO-seq.snakefile

@@ -586,6 +586,7 @@ rule check_last_base:
 
 
 # TODO: use Python to make the plot
+# This may remove dependency on R docopt
 rule plot_last_base:
     input:
         OPJ("{trimmer}", aligner, "mapped_C_elegans", "{lib}_{rep}_adapt_on_C_elegans_last_bases.txt")

PRO-seq/requirements.txt

+pysam
+pyBigWig
+scikit-learn
+matplotlib
+mandas
+seaborn
+husl
+rpy2
+libdeseq @ git+https://bioinfo_utils:uqiFbzWyBtzxYn7br82P@gitlab.pasteur.fr/bli/libdeseq.git
+libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
+libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git

RNA_Seq_Cecere/requirements.txt

+matplotlib
+numpy
+pandas
+scipy
+scikit-learn
+seaborn
+pyBigWig
+mappy
+rpy2
+libdeseq @ git+https://bioinfo_utils:uqiFbzWyBtzxYn7br82P@gitlab.pasteur.fr/bli/libdeseq.git
+libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
+libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git

small_RNA-seq/requirements.txt

+Cython
+pysam
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+pandas
+cytoolz
+libsmallrna @ git+https://bioinfo_utils:FjgTxcUGPsGVQ-yZZVyS@gitlab.pasteur.fr/bli/libsmallrna.git
+paraccumulators @ git+https://bioinfo_utils:EfTj-nvWDN84ZF_UzWPx@gitlab.pasteur.fr/bli/paraccumulators.git
+mappy
+pyBigWig
+scipy
+scikit-learn
+matplotlib
+seaborn
+deeptools
+libdeseq @ git+https://bioinfo_utils:uqiFbzWyBtzxYn7br82P@gitlab.pasteur.fr/bli/libdeseq.git
+libhts @ git+https://bioinfo_utils:DP-sqNot8AdsMek_KJiC@gitlab.pasteur.fr/bli/libhts.git
+libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git