Commit 5654f689 authored by khalid's avatar khalid
Browse files

Swich to cutadapt 4.0

parent 203d588a
......@@ -219,17 +219,8 @@
"make",
"make install"
],
cutadapt 2.10: [
"apt-get install python3-pip", # deja present
"cd /opt/biotools/",
"mkdir cutadapt-2.10",
"cd cutadapt-2.10",
"pip3 install --prefix=/opt/biotools/cutadapt-2.10 cutadapt==2.10",
"echo 'export PYTHONPATH=/opt/biotools/cutadapt-2.10/lib/python3.8/site-packages:$PYTHONPATH' >> /etc/environment",
],
frogs_cutadapt: [
# add to FROGS
"ln -s /opt/biotools/cutadapt-2.10/bin/cutadapt /opt/biotools/FROGS-3.2.3/libexec/."
cutadapt 4.0: [
"pip3 install cutadapt==4.0",
],
},
citations: {
......
......@@ -5,7 +5,7 @@
website: "https://cutadapt.readthedocs.io/en/stable/index.html",
git: "https://github.com/marcelm/cutadapt/",
description: "Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.",
version: "2.3",
version: "4.0",
documentation: "https://cutadapt.readthedocs.io/en/stable/index.html",
multiqc: "cutadapt",
commands:
......@@ -126,7 +126,7 @@
],
install: {
cutadapt: [
"pip3 install cutadapt==2.3",
"pip3 install cutadapt==4.0",
],
pigz: [
"apt-get install -y pigz"
......
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