Differences

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--- stringtie-software [2014/07/22 13:02] – created aorth
+++ stringtie-software [2015/08/04 09:02] – aorth
@@ Line 1: / Line 1: @@
 ====== stringtie ======
+StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
 ===== Information =====
-  * Version: 0.97
+  * Version: 1.0.4
   * Added: July, 2014
-  * Link: http://ccb.jhu.edu/software/stringtie/
+  * Updated: August, 2015
+  * Link: https://ccb.jhu.edu/software/stringtie/
 ===== Usage =====
 === See versions of stringtie which are available ===
-<code>module avail stringtie</code>
+<code>$ module avail stringtie</code>
+=== Load latest version and print help ===
+<code>$ module load stringtie/1.0.4
+$ stringtie -h</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-0.97.tar.gz
+<code>$ cd /tmp
-tar xf stringtie-0.97.tar.gz
+$ wget http://ccb.jhu.edu/software/stringtie/dl/stringtie-1.0.4.tar.gz
-cd stringtie-0.97
+$ scl enable devtoolset-3 bash
-scl enable devtoolset-1.1 bash
+$ tar xf stringtie-1.0.4.tar.gz
-sed -i 's/SEARCHDIRS := -I. -I${GDIR} -I${BAM}/SEARCHDIRS := -I. -I${GDIR} -I\/export\/apps\/samtools\/0.1.19\/include\/bam/' Makefile
+$ cd stringtie-1.0.4
-sed -i 's/LDFLAGS := -g -L${BAM} ${LFLAGS}/LDFLAGS := -g -L\/export\/apps\/samtools\/0.1.19\/lib ${LFLAGS}/' Makefile
+$ scl enable devtoolset-3 bash
-make release
+$ make release
-sudo mkdir -p /export/apps/stringtie/0.97/bin
+$ sudo mkdir -p /export/apps/stringtie/1.0.4/bin
-sudo cp stringtie /export/apps/stringtie/0.97/bin</code>
+$ sudo cp stringtie /export/apps/stringtie/1.0.4/bin
+$ sudo cp LICENSE README /export/apps/stringtie/1.0.4</code>