Merge pull request #15 from srividya22/master

added external dependency scripts for KBaseRNASeq service

Author: scanon

kb_cufflinks/install-cufflinks.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+dest=${TARGET-/kb/runtime}
+echo "using $dest as installation directory";
+mkdir -p $dest
+
+# downlownload version
+VERSION='2.2.1'
+rm -rf cufflinks-${VERSION}*
+wget "http://cole-trapnell-lab.github.io/cufflinks/assets/downloads/cufflinks-${VERSION}.Linux_x86_64.tar.gz"
+tar -xzvf cufflinks-${VERSION}.Linux_x86_64.tar.gz
+rm cufflinks-${VERSION}.Linux_x86_64.tar.gz
+# compile and copy binaries
+pushd cufflinks-${VERSION}.Linux_x86_64
+#make
+cp `find . -maxdepth 1 -perm -111 -type f` ${dest}/bin
+popd
+rm -rf cufflinks-${VERSION}.Linux_x86_64

kb_tophat/install-tophat.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+dest=${TARGET-/kb/runtime}
+echo "using $dest as installation directory";
+mkdir -p $dest
+
+# downlownload version
+VERSION='2.1.0'
+rm -rf tophat-${VERSION}*
+wget "https://ccb.jhu.edu/software/tophat/downloads/tophat-${VERSION}.Linux_x86_64.tar.gz"
+tar -xzvf tophat-${VERSION}.Linux_x86_64.tar.gz
+rm tophat-${VERSION}.Linux_x86_64.tar.gz
+# compile and copy binaries
+pushd tophat-${VERSION}.Linux_x86_64
+#make
+cp bam2fastx bam_merge bed_to_juncs contig_to_chr_coords fix_map_ordering gtf_juncs gtf_to_fasta juncs_db long_spanning_reads map2gtf prep_reads sam_juncs samtools_0.1.18 segment_juncs sra_to_solid tophat tophat2 tophat-fusion-post tophat_reports $dest/bin
+popd
+rm -rf tophat-${VERSION}.Linux_x86_64