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computers:bioinfo_server_configuration [2023/01/11 11:05] – [HTSeq] hychangcomputers:bioinfo_server_configuration [2025/06/30 12:37] (current) – [Velvet] chkuo
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>
  
Line 364: Line 371:
 ===== PAML ===== ===== PAML =====
   * Phylogenetic Analysis by Maximum Likelihood (PAML)   * Phylogenetic Analysis by Maximum Likelihood (PAML)
-  * [[http://abacus.gene.ucl.ac.uk/software/paml.html]]+  * [[http://abacus.gene.ucl.ac.uk/software/]]
  
 <code bash> <code bash>
-chkuo@koa[/usr/local]$ sudo wget http://abacus.gene.ucl.ac.uk/software/paml4.9h.tgz +# 2023/05/19 
-chkuo@koa[/usr/local]$ sudo tar xzf paml4.9h.tgz +chkuo@koa[/usr/local]$ sudo wget https://github.com/abacus-gene/paml/releases/download/v4.10.6/paml-4.10.6-linux-X86_64.tgz 
-chkuo@koa[/usr/local]$ sudo chown -R root:root paml4.9h +chkuo@koa[/usr/local]$ sudo tar xzf paml-4.10.6-linux-X86_64.tgz 
-chkuo@koa[/usr/local]$ sudo chmod -R 755 paml4.9h +chkuo@koa[/usr/local]$ sudo chown -R root:root paml-4.10.6 
-chkuo@koa[/usr/local]$ sudo rm /usr/local/paml4.9h/bin/*exe +chkuo@koa[/usr/local]$ sudo chmod -R 755 paml-4.10.6 
-chkuo@koa[/usr/local]$ cd /usr/local/paml4.9h/src +chkuo@koa[/usr/local]$ cd paml-4.10.6/src 
-chkuo@koa[/usr/local/paml4.9h/src]$ sudo make -f Makefile +chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo make -f Makefile 
-chkuo@koa[/usr/local/paml4.9h/src]$ sudo mv baseml basemlg chi2 codeml evolver mcmctree pamp yn00  ../bin +chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo rm *.o 
-chkuo@koa[/usr/local]$ sudo ln -s /usr/local/paml4.9h /usr/local/paml+chkuo@koa[/usr/local/paml-4.10.6/src]$ sudo mv baseml basemlg chi2 codeml evolver infinitesites mcmctree pamp yn00 ../bin
 </code> </code>
  
Line 482: Line 489:
 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>
  
Line 663: Line 673:
 ===== bbtools ===== ===== bbtools =====
   * BBMap short-read aligner and a bunch of tools (shell scripts)   * 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> <code bash>
Line 800: Line 810:
   * [[https://htseq.readthedocs.io/en/master/]]   * [[https://htseq.readthedocs.io/en/master/]]
   * HTSeq: High-throughput sequence analysis in Python   * HTSeq: High-throughput sequence analysis in Python
-  * Because using pip install is failed, so using apt install.+  * Using pip install failed, so using apt install.[[https://ubuntu.pkgs.org/20.04/ubuntu-universe-arm64/python3-htseq_0.11.2-2build1_arm64.deb.html|pkgs.org for python3-htseq]]
  
 <code bash> <code bash>
-hychang@koa:~$ sudo apt install python3-htseq +hychang@koa:[~]$ sudo apt install python3-htseq 
-[sudo] password for hychang:  +# [sudo] password for hychang:  
-Reading package lists... Done +# Reading package lists... Done 
-Building dependency tree        +# Building dependency tree        
-Reading state information... Done +# Reading state information... Done 
-E: Unable to locate package python3-htseq +# E: Unable to locate package python3-htseq 
-hychang@koa:~$ htseq-count --version +hychang@koa:[~]$ htseq-count --version 
-2.0.2+# 2.0.2 
 +hychang@koa:[~]$ whereis htseq-count 
 +# htseq-count: /usr/local/bin/htseq-count
 </code> </code>
  
Line 854: Line 866:
 </code> </code>
 ===== SPAdes ===== ===== SPAdes =====
-  * http://cab.spbu.ru/software/spades/+  * [[https://github.com/ablab/spades]]
  
 <code bash> <code bash>
Line 909: Line 921:
  
 ===== Velvet ===== ===== Velvet =====
-  * Sequence assembler for very short reads +  * [[https://github.com/dzerbino/velvet]]
-  * [[http://www.ebi.ac.uk/~zerbino/velvet/]]+
  
 <code bash> <code bash>
Line 954: Line 965:
  
 <code bash> <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 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> </code>
  
Line 1393: Line 1405:
 ===== SignalP ===== ===== SignalP =====
   * Predicts the presence and location of signal peptide cleavage sites in amino acid sequences.   * 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> <code bash>
Line 1480: Line 1509:
  
 <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.1673406335.txt.gz · Last modified: by hychang