From 49575178912e0721ac4bceca180624cfaf16e6fb Mon Sep 17 00:00:00 2001 From: Blaise Li <blaise.li__git@nsup.org> Date: Mon, 27 Jan 2020 15:29:06 +0100 Subject: [PATCH] Using auto-cythonizing 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 0467802..0ec6a30 160000 --- a/bam25prime +++ b/bam25prime @@ -1 +1 @@ -Subproject commit 0467802954cef4c07a1adfc4b9692bd9fdd6f792 +Subproject commit 0ec6a30646ddb06a6ff0bb91314515f029415985 diff --git a/libhts b/libhts index 6666fe7..fbbe4ad 160000 --- a/libhts +++ b/libhts @@ -1 +1 @@ -Subproject commit 6666fe7b98ac7538d2c524257892c3930eb34f52 +Subproject commit fbbe4ad34d94a039b7fdb01f32877c6d5d66512a diff --git a/small_RNA-seq/requirements.txt b/small_RNA-seq/requirements.txt index 398d43b..604e38c 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 @ git+https://github.com/blaiseli/pybedtools.git@auto_cythonize # pybedtools pysam paraccumulators @ git+https://bioinfo_utils:EfTj-nvWDN84ZF_UzWPx@gitlab.pasteur.fr/bli/paraccumulators.git -- GitLab