Differences

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

--- bcftools-software [2017/12/24 15:01] – aorth
+++ bcftools-software [2021/09/05 10:51] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 1.6
+  * Latest Version: 1.13
   * Added: September, 2015
-  * Updated: December, 2017
+  * Updated: September, 2021
   * Link: https://samtools.github.io/bcftools
@@ Line 14: / Line 14: @@
 <code>$ module avail bcftools</code>
-Load one version into your environment:
+Load one version into your environment and run it:
-<code>$ module load bcftools/1.6</code>
+<code>$ module load bcftools/1.13
+$ bcftools</code>
 ===== Installation ======
@@ Line 21: / Line 22: @@
 <code>$ cd /tmp
-$ wget https://github.com/samtools/bcftools/releases/download/1.6/bcftools-1.6.tar.bz2
+$ wget https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2
-$ tar xf bcftools-1.6.tar.bz2
+$ tar xf bcftools-1.13.tar.bz2
-$ cd bcftools-1.6
+$ cd bcftools-1.13
-$ ./configure --prefix=/export/apps/bcftools/1.6
+# install a newer compiler from Red Hat software collections
-$ make all all-htslib
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-$ sudo mkdir /export/apps/bcftools/1.6
+$ scl enable devtoolset-7 bash
-$ sudo chown aorth /export/apps/bcftools/1.6
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.13 --with-htslib=/export/apps/htslib/1.13
-$ make install install-htslib
+$ make
-$ sudo chown -R root:root /export/apps/bcftools/1.6</code>
+$ sudo mkdir -p /export/apps/bcftools/1.13
+$ sudo chown aorth /export/apps/bcftools/1.13
+$ make install
+sudo chown -R root:root /export/apps/bcftools/1.13</code>
+This links bcftools against a system-wide installation of htslib/1.13.