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--- computers:bioinfo_server_configuration [2023/05/19 17:25] – [PAML] chkuo
+++ computers:bioinfo_server_configuration [2025/06/30 12:37] (current) – [Velvet] 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 856: / Line 866: @@
 </code>
 ===== SPAdes =====
-  * http://cab.spbu.ru/software/spades/
+  * [[https://github.com/ablab/spades]]
 <code bash>
@@ Line 911: / Line 921: @@
 ===== Velvet =====
-  * Sequence assembler for very short reads
+  * [[https://github.com/dzerbino/velvet]]
-  * [[http://www.ebi.ac.uk/~zerbino/velvet/]]
 <code bash>
@@ Line 956: / Line 965: @@
 <code bash>
-# updated 2020/04/29 by chkuo; the previous version (also the version first installed on koa) was v0.4.8-beta
+# 2023/09/07; v0.4.9b -> v0.5.0; chkuo
+# 2020/04/29; v0.4.8b -> v0.4.9b; chkuo
 chkuo@koa[/usr/local]$ sudo git clone https://github.com/rrwick/Unicycler.git
-chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.4.9b
+chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.5.0
-chkuo@koa[/usr/local]$ cd unicycler-0.4.9b
+chkuo@koa[/usr/local]$ cd unicycler-0.5.0
-chkuo@koa[/usr/local/unicycler-0.4.9b]$ sudo python3 setup.py install
+chkuo@koa[/usr/local/unicycler-0.5.0]$ sudo python3 setup.py install
-chkuo@koa[/usr/local/unicycler-0.4.9b]$ unicycler --version
+chkuo@koa[/usr/local/unicycler-0.5.0]$ unicycler --version
-Unicycler v0.4.9b
+Unicycler v0.5.0
 </code>
@@ Line 1395: / Line 1405: @@
 ===== SignalP =====
   * Predicts the presence and location of signal peptide cleavage sites in amino acid sequences.
-  * Server: [[http://www.cbs.dtu.dk/services/SignalP/]]
+  * [[https://services.healthtech.dtu.dk/services/SignalP-6.0/]]
-  * Download: [[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp]]
+<code bash>
+# 2024/02/07
+# fast
+chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.fast.tar.gz
+chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_fast
+chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_fast/signalp-6-package/
+# slow
+chkuo@koa[/usr/local]$ sudo tar -xzvf signalp-6.0h.slow_sequential.tar.gz
+chkuo@koa[/usr/local]$ sudo chown -R root:root signalp6_slow_sequential
+chkuo@koa[/usr/local]$ sudo pip3 install /usr/local/signalp6_slow_sequential/signalp-6-package/
+chkuo@koa[/usr/local]$ which signalp6
+/usr/local/bin/signalp6
+chkuo@koa[/usr/local]$ signalp6 --version
+SignalP 6.0 Signal peptide prediction tool 6.0h
+</code>
 <code bash>
@@ Line 1482: / Line 1509: @@
 <code bash>
-chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/ParBLiSS/FastANI/releases/download/v1.1/fastani-Linux64-v1.1.zip
+# 2024/04/02
-chkuo@koa[/usr/local/bin]$ sudo unzip fastani-Linux64-v1.1.zip
+# note: v1.34 has some error message; use v1.33 for now
-Archive:  fastani-Linux64-v1.1.zip
+chkuo@koa[/usr/local/bin]$ sudo wget https://github.com/ParBLiSS/FastANI/releases/download/v1.33/fastANI-Linux64-v1.33.zip
-  inflating: fastANI
+chkuo@koa[/usr/local/bin]$ sudo unzip fastANI-Linux64-v1.33.zip
-   creating: __MACOSX/
+Archive:  fastANI-Linux64-v1.33.zip
-  inflating: __MACOSX/._fastANI
+  inflating: fastANI
-chkuo@koa[/usr/local/bin]$ sudo rm -r __MACOSX
+chkuo@koa[/usr/local/bin]$ sudo mv fastANI fastANI_v1.33
 </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>