Results for "Parallel Processing"
Bio-Scripts
➜ trinityrnaseq-Trinity-v2.6.6 git:(master) ✗ ./Trinity --seqType f...0:35:42 CMD: java -Xmx64m -XX:ParallelGCThreads=2 -jar /home/urbe/T...lean.fastq --pairs_together --PARALLEL_STATS Converting input fil...Converting input files. (in parallel)Monday, July 9, 2018: 10:51:2...2141 days ago
- ➜ bin git:(master) ✗ ./fastq-dump --help Usage: ./fastq-dump [options] [...]...n cSRA object, default is "SEQUENCE" PROCESSING Read Splitting...
2140 days ago
- jitendra@jitendra-UNLOCK-INSTALL[SNP] wget https://github.com/broadinstitute/gatk/releases/download/4...reates an index for a feature file, e.g. VCF or BED file. ParallelCopyGCSDirectoryIntoHDFSSpark (BETA Tool) Parallel c...
2089 days ago
Installing pb-assembly on Linux !
[jnarayan@hmem00 ~]$ module avail -------------------------------------------------------- /usr/share/Modules/mo...2016b GCC/4.8.2 parallel/2...2048 days ago
Installing Platypus on Ubuntu !
(py27) ➜ Tools git:(master) ✗ git clone https://github.com/andyrimmer/P...ntu1_amd64.deb ... Unpacking python3-dev (3.6.5-3ubuntu1) ... Processing triggers for mime-support (3.60ubuntu1) ... Processing triggers for desktop-file-uti...2033 days ago
- $ sudo apt-get install rakudo [sudo] password for jit: Reading packa...up nqp (2018.03+dfsg-2) ... Setting up rakudo (2018.03-1) ... Processing triggers for man-db (2.8.3-2ubuntu0.1) ... Processing triggers for libc-bin (2.27-3...
1565 days ago
Perl script to run in parellel !
#!/usr/bin/perl use strict; use warnings; use Parallel::ForkManager; use Bio::SeqIO; my ($sequence_data_ref) = parse_genom...); my %genome=%{$sequence_data_ref}; my $n_processes = 4; my $pm = Parallel::...1700 days ago
Find and replace in multifasta or fasta header with perl onliner
You have a fasta file and you want to replace: "|" You are told to replace that by "_" perl -i -p -e "s/\|/_/g" genome.fasta -i = inplace editing -p = loop over lines and print each line (after processing) -e = command line script1629 days ago
- $ sudo apt install npm Reading package lists... Done Building dependency tree...ath-is-absolute (1.0.0-1) ... Setting up node-builtin-modules (1.1.1-1) ... Processing triggers for man-db (2.8.3-2)...
1567 days ago
Bash script to download SRA file !
#We can use the sratoolkit to directly pull the sequence data (in paired FASTQ format)...any downstream tools, so it's necessary to put things into FASTQ for further processing. The --split-files part of th...1573 days ago
