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--- computers:bioinfo_server_configuration [2023/09/07 12:53] – [Unicycler] chkuo
+++ computers:bioinfo_server_configuration [2024/04/19 15:47] (current) – [MrBayes] chkuo
@@ Line 482: / Line 482: @@
 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 956: / Line 959: @@
 <code bash>
-# updated 2023/09/07 by chkuo; the previous version was v0.4.9b
+# 2023/09/07; v0.4.9b -> v0.5.0; chkuo
-# updated 2020/04/29 by chkuo; the 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 mv Unicycler unicycler-0.5.0
@@ Line 1396: / Line 1399: @@
 ===== 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 1483: / Line 1503: @@
 <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>