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--- htslib-software [2017/02/05 11:40] – joguya
+++ htslib-software [2021/09/05 10:17] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 1.3.2
+  * Latest Version: 1.13
   * Added: March, 2015
-  * Updated: February, 2017
+  * Updated: September, 2021
   * Link: https://github.com/samtools/htslib
 ===== Usage =====
-=== See versions of htslib which are available ===
+See versions of htslib which are available:
 <code>$ module avail htslib</code>
-=== Load and run htslib ===
+Load one version into your environment and run some common commands:
-<code>$ module load htslib/1.3.2 </code>
+<code>$ module load htslib/1.13
+$ tabix
+$ bgzip</code>
 ===== Installation ======
 Notes from the sysadmin during installation:
-<code>cd /tmp
+<code>$ cd /tmp
-$ wget -qO- "https://github.com/samtools/htslib/releases/download/1.3.2/htslib-1.3.2.tar.bz2" | tar xjv
+$ wget https://github.com/samtools/htslib/releases/download/1.13/htslib-1.13.tar.bz2
-$ sudo mkdir /export/apps/htslib/1.3.2/
+$ tar xf htslib-1.13.tar.bz2
-$ sudo chown -R joguya:joguya /export/apps/htslib/1.3.2/
+$ cd htslib-1.13
-LD_LIBRARY_PATH=/export/apps/curl/7.47.1/lib:$LD_LIBRARY_PATH LDFLAGS="-L/export/apps/curl/7.47.1/lib" CFLAGS="-I/export/apps/curl/7.47.1/include" ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/htslib/1.3.2/
+# install a newer compiler from Red Hat software collections
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
+$ scl enable devtoolset-7 bash
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/htslib/1.13
 $ make
+$ sudo mkdir -p /export/apps/htslib/1.13
+$ sudo chown aorth /export/apps/htslib/1.13
 $ make install
-$ sudo chown -R root:root /export/apps/htslib/1.3.2
+$ sudo chown -R root:root /export/apps/htslib/1.13</code>
-</code>