Differences

This shows you the differences between two versions of the page.

--- samtools-software [2017/06/30 14:40] – aorth
+++ samtools-software [2019/09/03 22:00] – 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: 1.9
   * Added: February, 2015
-  * Updated: February, 2017
+  * Updated: September, 2019
   * 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/1.9</code>
 ===== Installation =====
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ cd /tmp
+$ wget https://github.com/samtools/samtools/releases/download/1.9/samtools-1.9.tar.bz2
-$ wget https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2
+$ tar xf samtools-1.9.tar.bz2
-$ tar xf samtools-1.3.1.tar.bz2
+$ cd samtools-1.9
-$ cd samtools-1.3.1/
+# install a newer compiler from Red Hat software collections
-$ scl enable devtoolset-2 bash
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-$ sudo mkdir /export/apps/samtools/1.3.1
+$ scl enable devtoolset-7 bash
-$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.9 --with-htslib=/export/apps/htslib/1.9
-$ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1
+$ make
-$ make all install-htslib
+$ sudo mkdir -p /export/apps/samtools/1.9
-$ make install install-htslib
+$ sudo chown aorth /export/apps/samtools/1.9
-$ sudo chown -R root:root /export/apps/samtools/1.3.1
+$ make install
-</code>
+$ sudo chown -R root:root /export/apps/samtools/1.9</code>
+This links against htslib installed as a module in htslib/1.9.