From 3bd89b6a35a84831a5562958b01fe492049a949b Mon Sep 17 00:00:00 2001
From: Nicolas Descostes <nicolas.descostes@embl.it>
Date: Thu, 14 Apr 2022 17:33:20 +0200
Subject: [PATCH] try downloading directly from quay.io
---
.../mapping/bowtie2/Singularity.bowtie2-245 | 27 +++++--------------
1 file changed, 6 insertions(+), 21 deletions(-)
diff --git a/recipes/mapping/bowtie2/Singularity.bowtie2-245 b/recipes/mapping/bowtie2/Singularity.bowtie2-245
index 073616b..8b9822a 100644
--- a/recipes/mapping/bowtie2/Singularity.bowtie2-245
+++ b/recipes/mapping/bowtie2/Singularity.bowtie2-245
@@ -1,27 +1,12 @@
-BootStrap: docker
-From: ubuntu:hirsute
+Bootstrap: docker
+From: quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2
-%help
- This singularity install bowtie2 v2.4.5
+%runscript
+ echo "Running container quay.io/biocontainers/bowtie2:2.4.5--py36hfca12d5_2, Bowtie v2.4.5"
+ exec /bin/bash "$@"
%post
-
- # ~~~~~~ General setup and folder creation ~~~~~~ #
-
- apt-get update && apt-get install -y wget bzip2 debootstrap
-
- # ~~~~~ MINICONDA 3.4.0.5 ~~~~~ #
- wget https://repo.anaconda.com/miniconda/Miniconda3-4.7.12.1-Linux-x86_64.sh && \
- bash Miniconda3-4.7.12.1-Linux-x86_64.sh -b -p /conda && \
- rm -f Miniconda3-4.7.12.1-Linux-x86_64.sh
- export PATH="/conda/bin:${PATH}"
-
- # ~~~~~ bowtie2 2.4.5 ~~~~~ #
- conda install -y -c bioconda bowtie2=2.4.5
-
-%environment
- export PATH="${PATH}:/conda/bin"
+ mkdir /cluster /work /tsd /projects
%labels
Author Nicolas Descostes
- Version v0.0.1
--
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