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--- computers:bioinfo_server_configuration [2024/04/03 11:48] – [FastANI] chkuo
+++ computers:bioinfo_server_configuration [2024/12/20 23:51] (current) – [bbtools] chkuo
@@ Line 103: / Line 103: @@
 chkuo@koa[~]$ sudo pip3 install seqmagick
 Successfully installed seqmagick-0.7.0
+# install panda package on 2024/07/29
+hychang@koa[~]$ sudo pip3 install pandas
+Successfully installed pandas-1.3.5 pytz-2024.1
+hychang@koa[~]$ sudo pip3 -V
+pip 22.2.2 from /usr/local/lib/python3.7/dist-packages/pip (python 3.7)
 </code>
@@ Line 482: / Line 489: @@
 chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install
 # install mrbayes
-chkuo@koa[/usr/local]$ sudo wget https://github.com/NBISweden/MrBayes/raw/v3.2.6/mrbayes-3.2.6.tar.gz
+# 2024/04/19
-chkuo@koa[/usr/local]$ sudo tar xzf mrbayes-3.2.6.tar.gz
+# 3.2.6 -> 3.2.7
-chkuo@koa[/usr/local]$ sudo chown -R root:root mrbayes-3.2.6
+chkuo@koa[/usr/local]$ sudo wget https://github.com/NBISweden/MrBayes/releases/download/v3.2.7/mrbayes-3.2.7.tar.gz
-chkuo@koa[/usr/local]$ cd mrbayes-3.2.6/src
+chkuo@koa[/usr/local]$ sudo tar xzf mrbayes-3.2.7.tar.gz
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo autoconf
+chkuo@koa[/usr/local]$ sudo chown -R root:root mrbayes-3.2.7
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo ./configure --enable-mpi=yes
+chkuo@koa[/usr/local]$ cd mrbayes-3.2.7
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo make
+chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo ./configure --with-mpi
-chkuo@koa[/usr/local/mrbayes-3.2.6/src]$ sudo make install
+chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make
+chkuo@koa[/usr/local/mrbayes-3.2.7]$ sudo make install
+chkuo@koa[/usr/local/mrbayes-3.2.7]$ /usr/local/bin/mb -v
+Version:   3.2.7
 </code>
@@ Line 663: / Line 673: @@
 ===== bbtools =====
   * BBMap short-read aligner and a bunch of tools (shell scripts)
-  * [[https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/installation-guide/]]
+  * [[https://jgi.doe.gov/data-and-tools/software-tools/bbtools/]]
 <code bash>
@@ Line 1509: / Line 1519: @@
 </code>
+===== parallel =====
+  * GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
+  * http://www.gnu.org/software/parallel
+<code bash>
+# 2024/07/29
+hychang@koa[~]$ sudo apt install parallel
+hychang@koa[~]$ parallel --version
+GNU parallel 20161222
+Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016
+Ole Tange and Free Software Foundation, Inc.
+License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
+This is free software: you are free to change and redistribute it.
+GNU parallel comes with no warranty.
+Web site: http://www.gnu.org/software/parallel
+When using programs that use GNU Parallel to process data for publication
+please cite as described in 'parallel --citation'.
+</code>
+===== HH-suite =====
+  * The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
+  * https://manpages.ubuntu.com/manpages/lunar/man1/hhsearch.1.html
+<code bash>
+# 2024/07/29
+# note:
+hychang@koa[~]$ sudo apt install hhsuite
+hychang@koa[~]$ hhsearch
+HHsearch 3.0.0 (15-03-2015)
+Search a database of HMMs with a query alignment or query HMM
+(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
+Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (2005).
+Usage: hhsearch -i query -d database [options]
+...
+</code>