Upgrate SRA toolkit to 2.8.0

Author: sminot

Dockerfile

@@ -13,8 +13,11 @@ RUN git clone https://github.com/sstephenson/bats.git /tmp/bats && \
 ADD requirements.txt /tmp/requirements.txt
 RUN pip install -r /tmp/requirements.txt && rm /tmp/requirements.txt
 
-# Add binaries
-ADD bin/fastq-dump /usr/local/bin/fastq-dump
+# Add the AWS CLI binaries
+RUN cd /tmp && \
+    wget http://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/2.8.0/sratoolkit.2.8.0-ubuntu64.tar.gz && \
+    tar xzvf sratoolkit.2.8.0-ubuntu64.tar.gz && \
+    cp sratoolkit.2.8.0-ubuntu64/bin/fastq-dump /usr/local/bin/
 
 # Add join_paired_docs scripts
 ADD https://gist.githubusercontent.com/boydgreenfield/805ac27e0a6b9a5adea7/raw/eae0640ea0b6b02dbe6bf22b18af605d04ce91f6/join_paired_ends.py /scripts/

bin/fastq-dump

@@ -5,9 +5,9 @@
     [[ $V == Python\ 2.7* ]]
 }
 
-@test "fastq-dump v2.5.2" {
+@test "fastq-dump v2.8.0" {
     F=$(fastq-dump --version)
-    [[ $F == *2.5.2* ]]
+    [[ $F == *2.8.0* ]]
 }
 
 @test "AWS CLI 1.8.3" {