Differences

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--- bcftools-software [2016/03/29 12:31] – joguya
+++ bcftools-software [2021/09/05 10:51] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 1.3
+  * Latest Version: 1.13
   * Added: September, 2015
-  * Updated: March, 2016
+  * Updated: September, 2021
   * Link: https://samtools.github.io/bcftools
 ===== Usage =====
-=== See versions of bcftools which are available ===
+See versions of bcftools which are available:
 <code>$ module avail bcftools</code>
+Load one version into your environment and run it:
+<code>$ module load bcftools/1.13
+$ bcftools</code>
 ===== Installation ======
@@ Line 18: / Line 22: @@
 <code>$ cd /tmp
-$ wget https://github.com/samtools/bcftools/releases/download/1.2/bcftools-1.2.tar.bz2
+$ wget https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2
-$ tar xf bcftools-1.2.tar.bz2
+$ tar xf bcftools-1.13.tar.bz2
-$ cd bcftools-1.2
+$ cd bcftools-1.13
-$ scl enable devtoolset-3 bash
+# 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/bcftools/1.13 --with-htslib=/export/apps/htslib/1.13
 $ make
-$ sudo mkdir -p /export/apps/bcftools/1.2
+$ sudo mkdir -p /export/apps/bcftools/1.13
-$ sudo chown aorth /export/apps/bcftools/1.2
+$ sudo chown aorth /export/apps/bcftools/1.13
-$ make prefix=/export/apps/bcftools/1.2 install
+$ make install
-$ sudo chown -R root:root /export/apps/bcftools/1.2</code>
+sudo chown -R root:root /export/apps/bcftools/1.13</code>
+This links bcftools against a system-wide installation of htslib/1.13.