computers:bioinfo_server_configuration
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| Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
| computers:bioinfo_server_configuration [2024/07/29 17:17] – [Python] hychang | computers:bioinfo_server_configuration [2024/12/20 23:51] (current) – [bbtools] chkuo | ||
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| Line 107: | Line 107: | ||
| hychang@koa[~]$ sudo pip3 install pandas | hychang@koa[~]$ sudo pip3 install pandas | ||
| Successfully installed pandas-1.3.5 pytz-2024.1 | Successfully installed pandas-1.3.5 pytz-2024.1 | ||
| + | hychang@koa[~]$ sudo pip3 -V | ||
| + | pip 22.2.2 from / | ||
| </ | </ | ||
| Line 671: | 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:// | + | * [[https:// |
| <code bash> | <code bash> | ||
| Line 1525: | Line 1527: | ||
| # 2024/07/29 | # 2024/07/29 | ||
| hychang@koa[~]$ sudo apt install parallel | hychang@koa[~]$ sudo apt install parallel | ||
| - | [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 | ||
| - | 0 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:// | ||
| - | Get:2 http:// | ||
| - | 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 .../ | ||
| - | Unpacking sysstat (11.6.1-1ubuntu0.2) ... | ||
| - | Selecting previously unselected package parallel. | ||
| - | Preparing to unpack .../ | ||
| - | Adding ' | ||
| - | l' | ||
| - | Adding ' | ||
| - | rallel.moreutils.1.gz by parallel' | ||
| - | Unpacking parallel (20161222-1) ... | ||
| - | Setting up sysstat (11.6.1-1ubuntu0.2) ... | ||
| - | |||
| - | Creating config file / | ||
| - | update-alternatives: | ||
| - | auto mode | ||
| - | Created symlink / | ||
| - | ib/ | ||
| - | 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 | hychang@koa[~]$ parallel --version | ||
| GNU parallel 20161222 | GNU parallel 20161222 | ||
| Line 1585: | Line 1545: | ||
| ===== 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). | * 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:// |
| <code bash> | <code bash> | ||
| Line 1591: | Line 1551: | ||
| # note: | # note: | ||
| hychang@koa[~]$ sudo apt install hhsuite | hychang@koa[~]$ sudo apt install hhsuite | ||
| - | Reading package lists... Done | ||
| - | Building dependency tree | ||
| - | Reading state information... Done | ||
| - | The following additional packages will be installed: | ||
| - | ffindex hhsuite-data libffindex0 | ||
| - | The following NEW packages will be installed: | ||
| - | ffindex hhsuite hhsuite-data libffindex0 | ||
| - | 0 upgraded, 4 newly installed, 0 to remove and 1 not upgraded. | ||
| - | 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:// | ||
| - | Get:2 http:// | ||
| - | Get:3 http:// | ||
| - | Get:4 http:// | ||
| - | Fetched 3167 kB in 3s (953 kB/s) | ||
| - | Selecting previously unselected package libffindex0. | ||
| - | (Reading database ... 207758 files and directories currently installed.) | ||
| - | Preparing to unpack .../ | ||
| - | Unpacking libffindex0 (0.9.9.7-4) ... | ||
| - | Selecting previously unselected package ffindex. | ||
| - | Preparing to unpack .../ | ||
| - | Unpacking ffindex (0.9.9.7-4) ... | ||
| - | Selecting previously unselected package hhsuite-data. | ||
| - | Preparing to unpack .../ | ||
| - | Unpacking hhsuite-data (3.0~beta2+dfsg-3) ... | ||
| - | Selecting previously unselected package hhsuite. | ||
| - | Preparing to unpack .../ | ||
| - | 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) ... | ||
| - | |||
| hychang@koa[~]$ hhsearch | hychang@koa[~]$ hhsearch | ||
computers/bioinfo_server_configuration.1722244649.txt.gz · Last modified: by hychang