From 2611c0b56030f2943d166cce21e3d863424f7dce Mon Sep 17 00:00:00 2001
From: Phil Ewels <phil.ewels@scilifelab.se>
Date: Sun, 25 Jun 2017 16:47:42 +0200
Subject: [PATCH] Fix bwa tests. Add bowtie2-build to docker.

---
 .travis.yml                  |  4 ++--
 Dockerfile                   |  7 ++++---
 tests/docker_test.sh         |  4 ++--
 tests/docker_test_bwameth.sh | 19 ++++++++++---------
 4 files changed, 18 insertions(+), 16 deletions(-)

diff --git a/.travis.yml b/.travis.yml
index 8bb116f..dd6d133 100644
--- a/.travis.yml
+++ b/.travis.yml
@@ -19,5 +19,5 @@ env:
   - s=docker_test_bwameth
 
 script:
-  - "./${s}.sh"
-  - "./${s}.sh true" # Run again, building reference genome
+  - "./${s}.sh true"
+  - "./${s}.sh" # Run again, WITHOUT building reference genome
diff --git a/Dockerfile b/Dockerfile
index 3de2ccf..3b94fbc 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -65,14 +65,15 @@ RUN mkdir /opt/bowtie2 && \
     cd /opt/bowtie2/bowtie2-2.3.2/ && \
     make && \
     ln -s /opt/bowtie2/bowtie2-2.3.2/bowtie2 /usr/local/bin/bowtie2 && \
+    ln -s /opt/bowtie2/bowtie2-2.3.2/bowtie2-build /usr/local/bin/bowtie2-build && \
     rm /opt/bowtie2/bowtie2.zip
 
 # Install Bismark
 RUN mkdir /opt/Bismark && \
-    curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.17.0.zip -o /opt/Bismark/bismark.zip && \
+    curl -fsSL https://github.com/FelixKrueger/Bismark/archive/0.18.1.zip -o /opt/Bismark/bismark.zip && \
     unzip /opt/Bismark/bismark.zip -d /opt/Bismark && \
     rm /opt/Bismark/bismark.zip
-ENV PATH="/opt/Bismark/Bismark-0.17.0:${PATH}"
+ENV PATH="/opt/Bismark/Bismark-0.18.1:${PATH}"
 
 # Install Qualimap
 RUN mkdir /opt/Qualimap && \
@@ -104,4 +105,4 @@ RUN mkdir /opt/MethylDackel && \
     rm /opt/MethylDackel/MethylDackel.zip
 
 # Install MultiQC
-RUN pip install git+git://github.com/ewels/MultiQC.git
+RUN pip install multiqc
diff --git a/tests/docker_test.sh b/tests/docker_test.sh
index c43ed23..c9fae17 100755
--- a/tests/docker_test.sh
+++ b/tests/docker_test.sh
@@ -26,9 +26,9 @@ fi
 
 if [ -z $1]
 then
-    buildrefs="--fasta ${data_dir}/references/WholeGenomeFasta/genome.fa"
-else
     buildrefs="--bismark_index ${data_dir}/references/BismarkIndex/"
+else
+    buildrefs="--fasta ${data_dir}/references/WholeGenomeFasta/genome.fa"
 fi
 
 run_name="Test MethylSeq Run: "$(date +%s)
diff --git a/tests/docker_test_bwameth.sh b/tests/docker_test_bwameth.sh
index 461e1f6..1af0249 100755
--- a/tests/docker_test_bwameth.sh
+++ b/tests/docker_test_bwameth.sh
@@ -1,13 +1,5 @@
 #!/usr/bin/env bash
 
-script_path="../bwa-meth.nf"
-if [ -z $1]
-then
-    echo "No argument given, going to try to run ../bwa-meth.nf"
-else
-    script_path=$1
-fi
-
 data_path="/tmp"
 if [ -d "./test_data" ]
 then
@@ -32,7 +24,16 @@ else
     echo "Done"
 fi
 
-cmd="nextflow run $script_path -resume -profile testing --fasta ${data_dir}/references/WholeGenomeFasta/genome.fa --fasta_index ${data_dir}/references/WholeGenomeFasta/genome.fa.fai --reads \"${data_dir}/*.fastq.gz\""
+if [ -z $1]
+then
+    buildrefs="--fasta_index ${data_dir}/references/WholeGenomeFasta/genome.fa.fai --bwa_meth_index results/reference_genome/genome"
+else
+    buildrefs=""
+fi
+
+run_name="Test MethylSeq Run: "$(date +%s)
+
+cmd="nextflow run ../bwa-meth.nf -resume -profile testing --fasta ${data_dir}/references/WholeGenomeFasta/genome.fa  $buildrefs --reads \"${data_dir}/*.fastq.gz\""
 echo "Starting nextflow... Command:"
 echo $cmd
 echo "-----"