Commit 30730e63 authored by Blaise Li's avatar Blaise Li
Browse files

More requirements specified. Missing dir link.

parent 91c34cd9
......@@ -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 \\
......
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
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
......@@ -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
......@@ -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
......@@ -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
......
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
small_RNA-seq
\ No newline at end of file
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
......@@ -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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