Results for "benchmarking and designing tools"
Bio-Scripts
(JitMetaENV) ➜ JitMeta conda install grabseqs -c louiejtaylor -c bioconda -c conda-forge Collecting package metadata (current_repodata.json): done Solving environment: done ==> WARNING: A newer version of conda exists.1206 days ago
- ...groupinstall -y 'Development Tools' sudo yum install -y expat...t to install different Perls, and cd into it: # Note that it d...l into a subfolder named src, and untar...l API, VEP, OncoKB, and other tools we use here at MSKCC: curl -...5LIB to find these libraries, and set $PATH to use this Perl inst...
2134 days ago
Palindrome Simulation commands !
(base) ➜ palindromeAssemblySim more allCommands 3315 mutate.sh in= mutan...indromeSimulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illu...-s 10 -o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illu...E.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim...1725 days ago
Read a tab delimited file and search with perl
use strict; use warnings; use Data::Dumper; use Text::CSV; use IO::Handle; my $file = "/home/urbe/Tools/Alienomics_v0.1/Alienomics/output/intermediate_files/rRNA/refGene.megablast"; open my $fh, "[0]\n"; warn Dumper $row; # To see the structure }2514 days ago
Loop over with all files in a directory in bash
#!/bin/bash FILES=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/* ref=/media/Comp...cbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f...2321 days ago
Perl script to convert fastq to fasta file
#!/usr/bin/env perl use strict; use warnings; use Bio::Factory::EMBOSS; my $usag...::EMBOSS->new; my $seqret = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication objec...2241 days ago
- ...ntering directory '/home/urbe/Tools/bloomfilter' Making all in T...ntering directory '/home/urbe/Tools/bloomfilter' make[2]: Leavin...checking whether gcc understands -c and -o together... yes che...ntering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' mak...
2141 days ago
Perl script to run SATSUMA in loop !
#!/usr/bin/perl -w use strict; use File::Temp qw(tempfile); # Usage perl 1by1.pl...V2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SAT...ds") { my $idFile="palindrome_ids.txt"; open my $handle, '2130 days ago
- #!/bin/bash #set the path export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/bin export PATH=$PATH:/home/urbe/Tools/augustus-3.2.3/scripts export AUGUSTUS_CONFIG_PATH=/home/urbe/Tools/augustus-3.2.3/config #run...
2127 days ago
- ...lGCThreads=2 -jar /home/urbe/Tools/tri...L25.DS.fa 100 10 > /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/...7:43 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/...8:32 CMD: mkdir -p /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/...0 -v -shuffle Number of Commands: 29867 succeeded(29867) 100...
2117 days ago
