Merge pull request #148 from databio/dev

v0.8.0
refgenie · Dec 6, 2019 · 774bb25 · 774bb25
2 parents 4b9cb4d + 2b66518
commit 774bb25
Show file tree

Hide file tree

Showing 14 changed files with 1,178 additions and 291 deletions.
diff --git a/containers/Dockerfile_refgenie b/containers/Dockerfile_refgenie
@@ -12,8 +12,8 @@ MAINTAINER Nathan Sheffield <nathan@code.databio.org>
 
 # htslib 1.9 (tabix cmd)
 	RUN apt-get install -y libz-dev libncurses-dev
-  RUN wget -O ~/htslib.tar.gz https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar xjf ~/htslib.tar.gz && cd htslib-1.9 && ./configure && make && make install
-  ENV PATH="/htslib-1.9:${PATH}"
+    RUN wget -O ~/htslib.tar.gz https://github.com/samtools/htslib/releases/download/1.9/htslib-1.9.tar.bz2 && tar xjf ~/htslib.tar.gz && cd htslib-1.9 && ./configure && make && make install
+    ENV PATH="/htslib-1.9:${PATH}"
 
 # install samtools 1.3.1
 	RUN wget -O ~/samtools.bz2 https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
@@ -60,5 +60,8 @@ MAINTAINER Nathan Sheffield <nathan@code.databio.org>
 	ENV PATH="/bwa-0.7.17:${PATH}"
 
 # STAR 2.7.1a
-  RUN wget -O ~/STAR.tar.gz https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz && tar -xf ~/STAR.tar.gz && cd STAR-2.7.1a/source && make STAR
-  ENV PATH="/STAR-2.7.1a/source:${PATH}"
+    RUN wget -O ~/STAR.tar.gz https://github.com/alexdobin/STAR/archive/2.7.1a.tar.gz && tar -xf ~/STAR.tar.gz && cd STAR-2.7.1a/source && make STAR
+    ENV PATH="/STAR-2.7.1a/source:${PATH}"
+
+# GenomeTools 1.5.10
+    RUN apt-get install -y genometools