More requirements specified. Missing dir link.

CLIP/iCLIP.snakefile

@@ -198,6 +198,7 @@ rule demultiplex:
     benchmark:
         OPJ(log_dir, "demultiplex_benchmark.txt")
     shell:
+        # qaf_demux should be available here: https://gitlab.pasteur.fr/bli/qaf_demux
         """
         qaf_demux \\
             -i {input.fq_in} -g -o {params.demux_dir} \\
@@ -703,6 +704,7 @@ rule make_normalized_bigwig:
     bam2bigwig.sh: bedGraphToBigWig failed
     """
             try:
+                # bam2bigwig.sh should be installed with libhts
                 shell("""
                     bam2bigwig.sh {input.bam} {params.genome_binned} \\
                         {wildcards.lib}_{wildcards.rep} {wildcards.orientation} %s \\

CLIP/requirements.txt

+matplotlib
+pandas
+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
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git

Degradome-seq/requirements.txt

+numpy
+pandas
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/bli/libworkflows.git

PRO-seq/requirements.txt

@@ -9,3 +9,6 @@ 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
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+# extra dependencies for some rules
+deeptools

RNA_Seq_Cecere/requirements.txt

@@ -10,3 +10,4 @@ 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
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git

Ribo-seq/Ribo-seq.snakefile

@@ -63,6 +63,9 @@ from pickle import load
 from fileinput import input as finput
 from sys import stderr
 from subprocess import Popen, PIPE, CalledProcessError
+# Useful data structures
+from collections import OrderedDict as od
+from collections import defaultdict, Counter
 
 # Useful for functional style
 from itertools import chain, combinations, product, repeat, starmap
@@ -70,13 +73,10 @@ from functools import reduce
 from operator import or_ as union
 from cytoolz import concat, merge_with, take_nth
 
+
 def concat_lists(lists):
     return list(concat(lists))
 
-# Useful data structures
-from collections import OrderedDict as od
-from collections import defaultdict, Counter
-
 
 import warnings
 

Ribo-seq/requirements.txt

+cytoolz
+mappy
+pysam
+pyBigWig
+scipy
+scikit-learn
+matplotlib
+pandas
+seaborn
+libsmallrna @ git+https://bioinfo_utils:FjgTxcUGPsGVQ-yZZVyS@gitlab.pasteur.fr/bli/libsmallrna.git
+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
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+rpy2
+# extra dependencies for some rules
+deeptools

sRNA-seq

+small_RNA-seq
\ No newline at end of file

small_RNA-seq/requirements.txt

-Cython
-pysam
-pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
-pandas
+# dependencies of the snakefile itself
 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
+snakemake
 mappy
 pyBigWig
 scipy
 scikit-learn
 matplotlib
+pandas
 seaborn
-deeptools
+libsmallrna @ git+https://bioinfo_utils:FjgTxcUGPsGVQ-yZZVyS@gitlab.pasteur.fr/bli/libsmallrna.git
 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
+snakemake_wrappers @ git+https://bioinfo_utils:Ues9rP1tyfzs1zs5BzpY@gitlab.pasteur.fr/bli/snakemake_wrappers.git
+rpy2
+
+# extra dependencies for the sRNA-seq annotation script small_RNA_seq_annotate.py
+pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize"
+pysam
+paraccumulators @ git+https://bioinfo_utils:EfTj-nvWDN84ZF_UzWPx@gitlab.pasteur.fr/bli/paraccumulators.git
+# extra dependencies for some rules
+deeptools

small_RNA-seq/small_RNA-seq.snakefile

@@ -2723,6 +2723,7 @@ your deepTools settings and check your input files.
 bam2bigwig.sh: bedGraphToBigWig failed
 """
             try:
+                # bam2bigwig.sh is installed with libhts
                 shell("""
                     niceload --noswap bam2bigwig.sh {input.bam} {params.genome_binned} \\
                         {wildcards.lib}_{wildcards.rep} {wildcards.orientation} F \\