From 313d0ce7e9bc140054ca92ecee2b5c4ee9a54c7d Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Wed, 22 Jan 2020 15:15:47 +0100 Subject: [PATCH] Use main pybedtools. --- bam25prime | 2 +- libhts | 2 +- small_RNA-seq/requirements.txt | 3 ++- 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/bam25prime b/bam25prime index 19d7818..e196dc2 160000 --- a/bam25prime +++ b/bam25prime @@ -1 +1 @@ -Subproject commit 19d78189de09096be40ec4fa8569bc087093a4d2 +Subproject commit e196dc25c2725c932974444d76ee16097488dda0 diff --git a/libhts b/libhts index 2f362a3..e2deade 160000 --- a/libhts +++ b/libhts @@ -1 +1 @@ -Subproject commit 2f362a38b407f980718b61ac36c26afd41441504 +Subproject commit e2deadec42e7eb8a61d083c99cc6e7a7728de5e6 diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt index 6e99775..cac8780 100644 --- a/small_RNA-seq/requirements.txt +++ b/small_RNA-seq/requirements.txt @@ -15,7 +15,8 @@ libworkflows @ git+https://bioinfo_utils:tfuTQsSZWMtC5xXJNFJh@gitlab.pasteur.fr/ 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" +# pybedtools @ git+https://github.com/blaiseli/pybedtools.git@fix_missing_headers --global-option="cythonize" +pybedtools pysam paraccumulators @ git+https://bioinfo_utils:EfTj-nvWDN84ZF_UzWPx@gitlab.pasteur.fr/bli/paraccumulators.git # extra dependencies for some rules -- GitLab