Use main pybedtools.

bam25prime @ e196dc25

-Subproject commit 19d78189de09096be40ec4fa8569bc087093a4d2
+Subproject commit e196dc25c2725c932974444d76ee16097488dda0

libhts @ e2deadec

-Subproject commit 2f362a38b407f980718b61ac36c26afd41441504
+Subproject commit e2deadec42e7eb8a61d083c99cc6e7a7728de5e6

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