From 4b38e5c18c7f4b37fa77c79d7da8f1036437e440 Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Mon, 21 Oct 2019 18:23:04 +0200 Subject: [PATCH] Requirements for some workflows. --- PRO-seq/PRO-seq.snakefile | 1 + PRO-seq/requirements.txt | 11 +++++++++++ RNA_Seq_Cecere/requirements.txt | 12 ++++++++++++ small_RNA-seq/requirements.txt | 17 +++++++++++++++++ 4 files changed, 41 insertions(+) create mode 100644 PRO-seq/requirements.txt create mode 100644 RNA_Seq_Cecere/requirements.txt create mode 100644 small_RNA-seq/requirements.txt diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile index 02c8c78..7bf0fe8 100644 --- a/PRO-seq/PRO-seq.snakefile +++ b/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") diff --git a/PRO-seq/requirements.txt b/PRO-seq/requirements.txt new file mode 100644 index 0000000..fd5a36c --- /dev/null +++ b/PRO-seq/requirements.txt @@ -0,0 +1,11 @@ +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 diff --git a/RNA_Seq_Cecere/requirements.txt b/RNA_Seq_Cecere/requirements.txt new file mode 100644 index 0000000..2296ba1 --- /dev/null +++ b/RNA_Seq_Cecere/requirements.txt @@ -0,0 +1,12 @@ +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 diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt new file mode 100644 index 0000000..4550d98 --- /dev/null +++ b/small_RNA-seq/requirements.txt @@ -0,0 +1,17 @@ +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 -- GitLab