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computers:bioinfo_server_configuration [2023/10/02 12:14] – [SignalP] chkuocomputers:bioinfo_server_configuration [2024/07/31 11:13] (current) – [parallel] hychang
Line 103: Line 103:
 chkuo@koa[~]$ sudo pip3 install seqmagick chkuo@koa[~]$ sudo pip3 install seqmagick
 Successfully installed seqmagick-0.7.0 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> </code>
  
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 chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install chkuo@koa[/usr/local/beagle-lib-3.1.2]$ sudo make install
 # install mrbayes # 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> </code>
  
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 <code bash> <code bash>
-updated 2023/09/07 by chkuothe previous version was v0.4.9b +# 2023/09/07; v0.4.9b -> v0.5.0; chkuo 
-updated 2020/04/29 by chkuothe previous version (also the version first installed on koa) was v0.4.8-beta+# 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 git clone https://github.com/rrwick/Unicycler.git
 chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.5.0 chkuo@koa[/usr/local]$ sudo mv Unicycler unicycler-0.5.0
Line 1398: Line 1408:
   * [[https://services.healthtech.dtu.dk/services/SignalP-6.0/]]   * [[https://services.healthtech.dtu.dk/services/SignalP-6.0/]]
  
 +
 +
 +<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> <code bash>
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 <code bash> <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> </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>
computers/bioinfo_server_configuration.1696220067.txt.gz · Last modified: 2023/10/02 12:14 by chkuo