From 30730e63bdc07b525de2924c8f5cf2bd593e3e33 Mon Sep 17 00:00:00 2001
From: Blaise Li <blaise.li__git@nsup.org>
Date: Mon, 28 Oct 2019 11:07:53 +0100
Subject: [PATCH] More requirements specified. Missing dir link.
---
CLIP/iCLIP.snakefile | 2 ++
CLIP/requirements.txt | 5 +++++
Degradome-seq/requirements.txt | 4 ++++
PRO-seq/requirements.txt | 3 +++
RNA_Seq_Cecere/requirements.txt | 1 +
Ribo-seq/Ribo-seq.snakefile | 8 ++++----
Ribo-seq/requirements.txt | 17 +++++++++++++++++
sRNA-seq | 1 +
small_RNA-seq/requirements.txt | 20 +++++++++++++-------
small_RNA-seq/small_RNA-seq.snakefile | 1 +
10 files changed, 51 insertions(+), 11 deletions(-)
create mode 100644 CLIP/requirements.txt
create mode 100644 Degradome-seq/requirements.txt
create mode 100644 Ribo-seq/requirements.txt
create mode 120000 sRNA-seq
diff --git a/CLIP/iCLIP.snakefile b/CLIP/iCLIP.snakefile
index 3850f3e..dc5e72e 100644
--- a/CLIP/iCLIP.snakefile
+++ b/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 \\
diff --git a/CLIP/requirements.txt b/CLIP/requirements.txt
new file mode 100644
index 0000000..f128eab
--- /dev/null
+++ b/CLIP/requirements.txt
@@ -0,0 +1,5 @@
+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
diff --git a/Degradome-seq/requirements.txt b/Degradome-seq/requirements.txt
new file mode 100644
index 0000000..336115a
--- /dev/null
+++ b/Degradome-seq/requirements.txt
@@ -0,0 +1,4 @@
+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
diff --git a/PRO-seq/requirements.txt b/PRO-seq/requirements.txt
index f90c938..958e2df 100644
--- a/PRO-seq/requirements.txt
+++ b/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
diff --git a/RNA_Seq_Cecere/requirements.txt b/RNA_Seq_Cecere/requirements.txt
index 2296ba1..c63dab2 100644
--- a/RNA_Seq_Cecere/requirements.txt
+++ b/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
diff --git a/Ribo-seq/Ribo-seq.snakefile b/Ribo-seq/Ribo-seq.snakefile
index 479db04..4b0b89c 100644
--- a/Ribo-seq/Ribo-seq.snakefile
+++ b/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
diff --git a/Ribo-seq/requirements.txt b/Ribo-seq/requirements.txt
new file mode 100644
index 0000000..9ad752b
--- /dev/null
+++ b/Ribo-seq/requirements.txt
@@ -0,0 +1,17 @@
+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
diff --git a/sRNA-seq b/sRNA-seq
new file mode 120000
index 0000000..51a3c67
--- /dev/null
+++ b/sRNA-seq
@@ -0,0 +1 @@
+small_RNA-seq
\ No newline at end of file
diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt
index 4550d98..7d1c244 100644
--- a/small_RNA-seq/requirements.txt
+++ b/small_RNA-seq/requirements.txt
@@ -1,17 +1,23 @@
-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
diff --git a/small_RNA-seq/small_RNA-seq.snakefile b/small_RNA-seq/small_RNA-seq.snakefile
index 547017d..2546f71 100644
--- a/small_RNA-seq/small_RNA-seq.snakefile
+++ b/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 \\
--
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