Results for "Tools"

Bio-Scripts

  • Install grabseqs with conda !

    (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.

    1180 days ago

  • Install Perl Locally !

    ...CentOS system admins should run: sudo yum groupinstall -y 'Development Tools' sudo yum install -y expat-d...stall # Install dependencies for Ensembl API, VEP, OncoKB, and other tools we use here at MSKCC: curl -...

    2107 days ago

  • Palindrome Simulation commands !

    ...01.fasta > allPalindromeSimulated.fa 3319 ~/Tools/art_bin_MountRainier/art_illu...51 -f 100 -m 300 -s 10 -o paired_dat 3320 ~/Tools/art_bin_MountRainier/art_illu...e -x interleavedPE.fasta 3326 cd masurca; ~/Tools/MaSuRCA-3.2.3/bin/masurca sim...

    1698 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 }

    2488 days ago

  • Loop over with all files in a directory in bash

    ...Genomics/ncbi-genomes-2017-11-13/* ref=/media/ComparativeGenomics/ncbi-genomes-2017-11-13/GCA_000196735.1_ASM19673v1_genomic.fna path=/home/urbe/Tools/SATSUMA/satsuma-code-0 for f...

    2294 days ago

  • Perl script to convert fastq to fasta file

    ...e; my $outfile = shift or die $usage; my $factory = Bio::Factory::EMBOSS->new; my $seqret = $factory->program('seqret'); # $seqret is a Bio::Tools::Run::EMBOSSApplication objec...

    2214 days ago

  • BloomFilter

    Tools git:(master) ✗ git clone git:...ing connectivity... done. ➜ Tools git:(master) ✗ cd bloomfilter...ntering directory '/home/urbe/Tools/bloomfilter' Making all in T...ntering directory '/home/urbe/Tools/bloomfilter' make[2]: Leavin...ntering directory '/home/urbe/Tools/bloomfilter/Tests/AdHoc' mak...

    2114 days ago

  • Perl script to run SATSUMA in loop !

    ...$seqfile=""; my $queryfile = "genome.fasta"; # Ur query genome my $tarfile = "renamedAdinetaV2.fa"; #Ur target file my $satsumaLoc="/home/urbe/Tools/SATSUMA/satsuma-code-0"; # Lo...

    2103 days ago

  • Bash script to run Busco2 !

    ...!/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...

    2100 days ago

  • Running Trinity on RNA-seq !

    ...(0 seconds) CMD: /home/urbe/Tools/trinityrnaseq-Trinity-v2.6.6/...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/...

    2090 days ago