Differences

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--- bcftools-software [2017/02/05 11:42] – [Installation] joguya
+++ bcftools-software [2021/09/05 10:49] – aorth
@@ Line 4: / Line 4: @@
 ===== Information =====
-  * Latest Version: 1.3.1
+  * Latest Version: 1.13
   * Added: September, 2015
-  * Updated: February, 2017
+  * 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:
+<code>$ module load bcftools/1.13</code>
 ===== Installation ======
@@ Line 18: / Line 21: @@
 <code>$ cd /tmp
-$ wget -qO- https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 | tar xjv
+$ wget https://github.com/samtools/bcftools/releases/download/1.13/bcftools-1.13.tar.bz2
-$ cd bcftools-1.3.1
+$ tar xf bcftools-1.13.tar.bz2
-$ scl enable devtoolset-3 bash
+$ cd bcftools-1.13
-$ sudo mkdir /export/apps/bcftools/1.3.1
+# install a newer compiler from Red Hat software collections
-$ HTSDIR=/export/apps/htslib/1.3.2 make
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-$ make prefix=/export/apps/bcftools/1.3.1 install
+$ scl enable devtoolset-7 bash
-$ sudo chown -R root:root /export/apps/bcftools/1.3.1
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/bcftools/1.13 --with-htslib=/export/apps/htslib/1.13
-</code>
+$ make
+$ 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.