Differences

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--- samtools-software [2017/06/30 14:40] – aorth
+++ samtools-software [2018/06/01 19:31] – aorth
@@ Line 2: / Line 2: @@
 samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-  * Latest Version: 1.3.1
+  * Latest Version: 1.8
   * Added: February, 2015
-  * Updated: February, 2017
+  * Updated: June, 2018
   * Link: http://www.htslib.org
@@ Line 14: / Line 14: @@
 Load a particular version of samtools:
-<code>$ module load samtools/1.3.1</code>
+<code>$ module load samtools/1.8</code>
 ===== Installation =====
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ cd /tmp
+$ wget https://github.com/samtools/samtools/releases/download/1.8/samtools-1.8.tar.bz2
-$ wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
+$ tar xf samtools-1.8.tar.bz2
-$ tar xf samtools-1.3.1.tar.bz2
+$ cd samtools-1.8
-$ cd samtools-1.3.1/
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.8 --with-htslib=/export/apps/htslib/1.8
-$ scl enable devtoolset-2 bash
+$ make
-$ sudo mkdir /export/apps/samtools/1.3.1
+$ sudo mkdir /export/apps/samtools/1.8
-$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1
+$ sudo chown aorth:aorth /export/apps/samtools/1.8
-$ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1
+$ make install
-$ make all install-htslib
+$ sudo chown -R root:root /export/apps/samtools/1.8</code>
-$ make install install-htslib
-$ sudo chown -R root:root /export/apps/samtools/1.3.1
+This links against a system-wide version of htslib/1.8.
-</code>