Differences

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--- bedtools-software [2016/06/22 06:41] – [Information] joguya
+++ bedtools-software [2023/02/13 14:17] – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Version: 2.25.0
+  * Version: 2.29.0
   * Added: January, 2013
-  * Updated: June, 2016
+  * Updated: September, 2019
   * Link: https://bedtools.readthedocs.io/en/latest/
@@ Line 15: / Line 15: @@
 <code>$ module avail bedtools</code>
-Load bedtools
+Load one version into your environment and run it:
-<code>$ module load bedtools/2.25.0</code>
+<code>$ module load bedtools/2.29.0
+$ bedtools</code>
 ===== Installation ======
@@ Line 22: / Line 23: @@
 Notes from the sysadmin during installation:
-<code>
+<code>$ cd /tmp
-$ cd /tmp/
+$ wget https://github.com/arq5x/bedtools2/releases/download/v2.29.0/bedtools-2.29.0.tar.gz
-$ wget https://github.com/arq5x/bedtools2/releases/download/v2.25.0/bedtools-2.25.0.tar.gz
+$ tar xf bedtools-2.29.0.tar.gz
-$ tar -xvf bedtools-2.25.0.tar.gz
+$ cd bedtools2
-$ scl enable devtoolset-2 bash
+# added in 2023-02 while re-compiling on CentOS Stream 8
-$ sudo mkdir /export/apps/bedtools/2.25.0/
+$ sed -i 's/python/python3/' Makefile
-$ sudo chown -R joguya:joguya /export/apps/bedtools/2.25.0/
-$ sed -i 's#prefix = /usr/local#prefix = /export/apps/bedtools/2.25.0#' Makefile
 $ make
-$ make install
+$ sudo mkdir -p /export/apps/bedtools/2.29.0
-$ sudo chown -R root:root /export/apps/bedtools/2.25.0/
+$ sudo chown aorth /export/apps/bedtools/2.29.0
-</code>
+$ sudo mkdir -p /export/apps/bedtools/2.29.0
+$ make install prefix=/export/apps/bedtools/2.29.0
+$ sudo chown -R root:root /export/apps/bedtools/2.29.0</code>