Differences

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--- computers:bioinfo_server_configuration [2024/07/29 16:36] – hychang
+++ computers:bioinfo_server_configuration [2024/12/20 23:51] (current) – [bbtools] 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 666: / 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 1514: / Line 1521: @@
 ===== parallel =====
-  * 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
-# note: Web site: http://www.gnu.org/software/parallel
+hychang@koa[~]$ sudo apt install parallel
-hychang@koa:~$ sudo apt install parallel
+hychang@koa[~]$ parallel --version
-[sudo] password for hychang:
-Reading package lists... Done
-Building dependency tree
-Reading state information... Done
-The following additional packages will be installed:
-  sysstat
-Suggested packages:
-  isag
-The following NEW packages will be installed:
-  parallel sysstat
-upgraded, 2 newly installed, 0 to remove and 1 not upgraded.
-Need to get 556 kB of archives.
-After this operation, 2221 kB of additional disk space will be used.
-Do you want to continue? [Y/n] Y
-Get:1 http://archive.ubuntu.com/ubuntu bionic/universe amd64 parallel all 20161222-1 [260 kB]
-Get:2 http://security.ubuntu.com/ubuntu bionic-security/main amd64 sysstat amd64 11.6.1-1ubuntu0.2 [295 kB]
-Fetched 556 kB in 2s (275 kB/s)
-Preconfiguring packages ...
-Selecting previously unselected package sysstat.
-(Reading database ... 207671 files and directories currently installed.)
-Preparing to unpack .../sysstat_11.6.1-1ubuntu0.2_amd64.deb ...
-Unpacking sysstat (11.6.1-1ubuntu0.2) ...
-Selecting previously unselected package parallel.
-Preparing to unpack .../parallel_20161222-1_all.deb ...
-Adding 'diversion of /usr/bin/parallel to /usr/bin/parallel.moreutils by paralle
-l'
-Adding 'diversion of /usr/share/man/man1/parallel.1.gz to /usr/share/man/man1/pa
-rallel.moreutils.1.gz by parallel'
-Unpacking parallel (20161222-1) ...
-Setting up sysstat (11.6.1-1ubuntu0.2) ...
-Creating config file /etc/default/sysstat with new version
-update-alternatives: using /usr/bin/sar.sysstat to provide /usr/bin/sar (sar) in
- auto mode
-Created symlink /etc/systemd/system/multi-user.target.wants/sysstat.service → /l
-ib/systemd/system/sysstat.service.
-Setting up parallel (20161222-1) ...
-Processing triggers for systemd (237-3ubuntu10.57) ...
-Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
-Processing triggers for ureadahead (0.100.0-21) ...####################################.......]
-ureadahead will be reprofiled on next reboot
-hychang@koa:~$ parallel --version
 GNU parallel 20161222
 Copyright (C) 2007,2008,2009,2010,2011,2012,2013,2014,2015,2016
@@ Line 1579: / Line 1543: @@
-===== hh suite =====
+===== HH-suite =====
-  * 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: Web site:
+# note:
-hychang@koa:~$ sudo apt install hhsuite
+hychang@koa[~]$ sudo apt install hhsuite
-Reading package lists... Done
+hychang@koa[~]$ hhsearch
-Building dependency tree
-Reading state information... Done
+HHsearch 3.0.0 (15-03-2015)
-The following additional packages will be installed:
+Search a database of HMMs with a query alignment or query HMM
-  ffindex hhsuite-data libffindex0
+(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser
-The following NEW packages will be installed:
+Soding, J. Protein homology detection by HMM-HMM comparison. Bioinformatics 21:951-960 (2005).
-  ffindex hhsuite hhsuite-data libffindex0
-upgraded, 4 newly installed, 0 to remove and 1 not upgraded.
+Usage: hhsearch -i query -d database [options]
-Need to get 3167 kB of archives.
+...
-After this operation, 14.5 MB of additional disk space will be used.
-Do you want to continue? [Y/n] Y
-Get:1 http://archive.ubuntu.com/ubuntu bionic/universe amd64 libffindex0 amd64 0.9.9.7-4 [16.7 kB]
-Get:2 http://archive.ubuntu.com/ubuntu bionic/universe amd64 ffindex amd64 0.9.9.7-4 [31.4 kB]
-Get:3 http://archive.ubuntu.com/ubuntu bionic/universe amd64 hhsuite-data all 3.0~beta2+dfsg-3 [2152 kB]
-Get:4 http://archive.ubuntu.com/ubuntu bionic/universe amd64 hhsuite amd64 3.0~beta2+dfsg-3 [967 kB]
-Fetched 3167 kB in 3s (953 kB/s)
-Selecting previously unselected package libffindex0.
-(Reading database ... 207758 files and directories currently installed.)
-Preparing to unpack .../libffindex0_0.9.9.7-4_amd64.deb ...
-Unpacking libffindex0 (0.9.9.7-4) ...
-Selecting previously unselected package ffindex.
-Preparing to unpack .../ffindex_0.9.9.7-4_amd64.deb ...
-Unpacking ffindex (0.9.9.7-4) ...
-Selecting previously unselected package hhsuite-data.
-Preparing to unpack .../hhsuite-data_3.0~beta2+dfsg-3_all.deb ...
-Unpacking hhsuite-data (3.0~beta2+dfsg-3) ...
-Selecting previously unselected package hhsuite.
-Preparing to unpack .../hhsuite_3.0~beta2+dfsg-3_amd64.deb ...
-Unpacking hhsuite (3.0~beta2+dfsg-3) ...
-Setting up hhsuite-data (3.0~beta2+dfsg-3) ...
-Setting up libffindex0 (0.9.9.7-4) ...
-Setting up ffindex (0.9.9.7-4) ...
-Setting up hhsuite (3.0~beta2+dfsg-3) ...
-Processing triggers for man-db (2.8.3-2ubuntu0.1) ...
-Processing triggers for libc-bin (2.27-3ubuntu1.5) ...
 </code>