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Feature/bwamem2 #54

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merged 8 commits into from
Feb 14, 2020
Merged

Feature/bwamem2 #54

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5b7812d
Changes required to provide a merging script which is aware of mmQc
keiranmraine Dec 16, 2019
83b7a15
Add travis verification of new script install
keiranmraine Dec 16, 2019
f164bc1
switch to more formal path lookups
keiranmraine Dec 17, 2019
4904f77
Detail changes and fix some markdown errors
keiranmraine Dec 20, 2019
0b3c0c3
This would do a full switch to bwa-mem2, probably want it to be optio…
keiranmraine Feb 4, 2020
62f70a1
Show content of log in direct output as well as file it is from
keiranmraine Feb 8, 2020
7b6f57a
bwa-mem2 and efficiency in merging steps
keiranmraine Feb 8, 2020
355b204
install bwa-mem2 in setup.sh also, as well as move URL for release in…
keiranmraine Feb 10, 2020
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install bwa-mem2 in setup.sh also, as well as move URL for release in… 
…to Dockerfile for other methods
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@keiranmraine
keiranmraine committed Feb 10, 2020
commit 355b2043aeed1d81e1321e60c4e849974eeffbd8
1 change: 1 addition & 0 deletions Dockerfile
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Expand Up @@ -3,6 +3,7 @@ FROM quay.io/wtsicgp/cgpbigwig:1.1.0 as builder
USER root

ARG BBB2_URL="https://gitlab.com/german.tischler/biobambam2/uploads/178774a8ece96d2201fcd0b5249884c7/biobambam2-2.0.146-release-20191030105216-x86_64-linux-gnu.tar.xz"
ARG BWAMEM2_URL="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"
ARG STADEN="https://iweb.dl.sourceforge.net/project/staden/staden/2.0.0b11/staden-2.0.0b11-2016-linux-x86_64.tar.gz"
ARG VER_BIODBHTS="3.01"
ARG VER_BWA="v0.7.17"
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2 changes: 1 addition & 1 deletion build/opt-build.sh
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Expand Up @@ -109,7 +109,7 @@ fi

## build BWA-mem2 (tar.gz)
if [ ! -e $SETUP_DIR/bwa2.success ]; then
curl -sSL https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2 > distro.tar.bz2
curl -sSL $BWAMEM2_URL > distro.tar.bz2
rm -rf distro/*
tar --strip-components 1 -C distro -jxf distro.tar.bz2
cp distro/bwa-mem2* $INST_PATH/bin/.
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13 changes: 13 additions & 0 deletions setup.sh
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@@ -1,6 +1,7 @@
#!/bin/bash

SOURCE_BWA="https://github.com/lh3/bwa/archive/v0.7.17.tar.gz"
SOURCE_BWAMEM2="https://github.com/bwa-mem2/bwa-mem2/releases/download/v2.0pre2/bwa-mem2-2.0pre2_x64-linux.tar.bz2"

# for bamstats and Bio::DB::HTS
SOURCE_HTSLIB="https://github.com/samtools/htslib/releases/download/1.7/htslib-1.7.tar.bz2"
Expand Down Expand Up @@ -202,6 +203,18 @@ else
touch $SETUP_DIR/bwa.success
fi

## build BWA-mem2 (tar.gz)
cd $SETUP_DIR
echo -n "Building bwa-mem2 ..."
if [ ! -e $SETUP_DIR/bwa2.success ]; then
curl -sSL $SOURCE_BWAMEM2 > distro.tar.bz2
rm -rf distro/*
tar --strip-components 1 -C distro -jxf distro.tar.bz2
cp distro/bwa-mem2* $INST_PATH/bin/.
rm -rf distro.* distro/*
touch $SETUP_DIR/bwa2.success
fi

echo -n "Building biobambam2 ..."
if [ -e $SETUP_DIR/biobambam2.success ]; then
echo " previously installed ..."
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