diff --git a/PRO-seq/PRO-seq.snakefile b/PRO-seq/PRO-seq.snakefile
index 02c8c784c0e940bf13e70c518f5012e999cb4bbc..7bf0fe83f5d0535bf1ee356a23a8858b397bf5f6 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 0000000000000000000000000000000000000000..fd5a36cc0ebe8a57900ddd8e87ad99744b62952d
--- /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 0000000000000000000000000000000000000000..2296ba11461c45af33bb0624f5f447f0962ef2de
--- /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 0000000000000000000000000000000000000000..4550d9821090bea7c640498c4e169bdb67be7a5e
--- /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