Commit 4b38e5c1 authored by Blaise Li's avatar Blaise Li
Browse files

Requirements for some workflows.

parent af8998bf
...@@ -586,6 +586,7 @@ rule check_last_base: ...@@ -586,6 +586,7 @@ rule check_last_base:
# TODO: use Python to make the plot # TODO: use Python to make the plot
# This may remove dependency on R docopt
rule plot_last_base: rule plot_last_base:
input: input:
OPJ("{trimmer}", aligner, "mapped_C_elegans", "{lib}_{rep}_adapt_on_C_elegans_last_bases.txt") OPJ("{trimmer}", aligner, "mapped_C_elegans", "{lib}_{rep}_adapt_on_C_elegans_last_bases.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
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
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
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