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computers:bioinfo_server_configuration [2023/01/11 15:04] – [HTSeq] hychangcomputers:bioinfo_server_configuration [2024/04/19 15:47] (current) – [MrBayes] chkuo
Line 364: Line 364:
 ===== 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 482:
 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 800: Line 803:
   * [[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
-  * Using pip install is 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]]+  * 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>
Line 956: Line 959:
  
 <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 1395: Line 1399:
 ===== 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 1482: Line 1503:
  
 <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>
  
computers/bioinfo_server_configuration.1673420640.txt.gz · Last modified: 2023/01/11 15:04 by hychang