Results for "Command Line"
Bio-Scripts
Bash oneliner to extract all ids from a multifasta file
#List of ids - one per line in allIds.txt $ awk 'BEGIN{while((getline0)l[">"$1]=1}/^>/{f=!l[$1]}f' seq.fa # You can play with this f=!l[$1 ] if wanted to extract or not extract the ids1560 days ago
Install Parrot Virtual Machine !
...unless you passed in the `--ask' flag on the command line, in which case I'll prompt yo.../Parrot/Config/Generated.pm"? at Configure.pl line 84. Deleting gcov-generated...f LLVM installed............skipped. auto::inline - Does your compiler s...1559 days ago
Install Python locally on shared Linux server !
...the source following its guideline ./configure --prefix=$HOME/py...t the #related output of make command, by default it is in the /usr...he default, if we type python command, it will use the default pyth...rofile and add the #following line: export PATH=$HOME/.local/...2120 days ago
- ...ERTIES/FILE gatk forwards commands to GATK and adds some sugar...--spark-submit-command may be specified to control t...output the generated command line without running it --java...nd host reads PathSeqPipelineSpark...
2097 days ago
- ➜ upgrade_oh_my_zsh Updating Oh My Zsh remote: Counting objects: 484, done. remote: Compressing objects: 100%...plugins/coffee/_coffee | 4 +- plugins/command-not-found/comm...
2096 days ago
Installing pb-assembly on Linux !
...libreadline/6.3-foss-2016a Armadillo/2.4.4-...libreadline/6.3-foss-2016b arpack-ng/3.3.0-...1 bioconda pbcommand: 1.1.1-py27h...Time: 0:00:00 21.90 MB/s pbcommand-1.1. 100% |###############...2056 days ago
- (denovo_asm) [jnarayan@hmem00 ~]$ git clone https://github.com/cdunn2001/git-sym.git fatal: destination path 'git-s...sers/j/n/jnarayan/FALCON-examples/.git-sym') git: 'check-ignore' is not a git comm...
2056 days ago
- ...[-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~~~~~~~~~~~~...-Wunused-result] fgets( line, MAXLINE, fp); ^~~~~~~~~~~.../shared/constants -c -o ReadCommandLineNPK.o ReadCommandLineNPK.c ReadCommandLineN..../src/shared/rng -c -o read_command_line.o read_command_line.c read_c...
2048 days ago
Installing Platypus on Ubuntu !
...pgrading via the 'pip install --upgrade pip' command. (py27) ➜ Platypus git:(m...‘MIN_PARTIAL_MATCH’ is static but used in inline function ‘foundmatch’ which is n...c: At top level: cc1: warning: unrecognized command line option ‘-Wno-unneeded-interna...2041 days ago
Setting up falconUnzip conda environments for genome assembly !
...78 KB conda-forge linecache2-1.0.0 |...22 KB bioconda pbcommand-1.1.1 |..._3 conda-forge linecache2: 1.0.0-py_1...es, intended only for command-line users, and # # possib...2011 days ago
