Raoul J.P. Bonnal rjpbonnal
rjpbonnal
/ freenas_11.2_update_fix_vnets
Created
March 2, 2019 16:37
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| /bin/sh -c 'export JAILS="$(iocage list -h | cut -f 2)"; for jail in $JAILS; do iocage set vnet_default_interface=auto $jail; done; iocage set vnet_default_intercace=auto default' |
rjpbonnal
/ scanpy_137_packages.txt
Created
February 4, 2019 16:00
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| Package Version | |
| ------------------------ ----------- | |
| alabaster 0.7.12 | |
| anndata 0.6.18 | |
| astropy 3.1.1 | |
| atomicwrites 1.3.0 | |
| attrs 18.2.0 | |
| Babel 2.6.0 | |
| backcall 0.1.0 | |
| certifi 2018.11.29 |
rjpbonnal
/ TCGAanalyze_RemoveReplicateSamples.R
Created
November 30, 2017 17:43
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| # http://gdac.broadinstitute.org/runs/sampleReports/latest/READ_Replicate_Samples.html | |
| TCGAanalyze_RemoveReplicateSamples<-function(tabDF, typesample){ | |
| tabDF.typesample <- tabDF[, TCGAquery_SampleTypes(colnames(tabDF), typesample=typesample)] | |
| # detect duplicated patient for typesample | |
| tabDF.typesample.duplicated = duplicated(tabDF.typesample$patient) | |
| if (sum(tabDF.typesample.duplicated)>0){ | |
| tabDF.typesample.not_duplicated = !(tabDF.typesample$patient %in% tabDF.typesample[,tabDF.typesample.duplicated]$patient) | |
| # print(tabDF.typesample$patient[tabDF.typesample.duplicated]) | |
| # print(class(tabDF.typesample$patient[tabDF.typesample.duplicated])) | |
| barcodes_solved_duplication=sapply(tabDF.typesample$patient[tabDF.typesample.duplicated],function(patient, dataset){ |
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| ;;; GNU Guix --- Functional package management for GNU | |
| ;;; Copyright © 2015, 2016 Ricardo Wurmus <rekado@elephly.net> | |
| ;;; Copyright © 2015 Vicente Vera Parra <vicentemvp@gmail.com> | |
| ;;; Copyright © 2016 Andreas Enge <andreas@enge.fr> | |
| ;;; Copyright © 2016 Efraim Flashner <efraim@flashner.co.il> | |
| ;;; Copyright © 2016 Pjotr Prins <pjotr.guix@thebird.nl> | |
| ;;; Copyright © 2016 Roel Janssen <roel@gnu.org> | |
| ;;; Copyright © 2016 Ben Woodcroft <donttrustben@gmail.com> | |
| ;;; | |
| ;;; This file is part of GNU Guix. |
rjpbonnal
/ gist:fdc94a2637a208d47a03
Created
January 13, 2016 14:26
Scala Create an iterator using a Stream over 2 "aligned" files
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| test("Detect barcodes in forward and reverse reads in Fastq format") { | |
| val readerR1 = new FastqReader(new java.io.File(getClass.getResource("/R1.fastq.gz").getPath)) | |
| val readerR2 = new FastqReader(new java.io.File(getClass.getResource("/R2.fastq.gz").getPath)) | |
| var list = List[String]() | |
| case class Reads( r1: FastqRecord, r2: FastqRecord) | |
| val stream: Stream[Reads]= { | |
| def reads(readerR1: FastqReader, readerR2: FastqReader): Stream[Reads] = { | |
| readerR1.hasNext() && readerR2.hasNext() match { |
rjpbonnal
/ trinity-pipeline-template.pbs
Last active
August 29, 2015 14:26
The file is an example of the command lines used to run Trinity and PASA, at the time of the original work (“LincRNAs landscape in human lymphocytes highlights modulation of T cell differentiation by linc-MAF-4” by Ranzani V. et al.) Recently Trinity and PASA were updated, the current command lines and options can differ.
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| #!/bin/bash | |
| # Copyright (C) 2015 INGM | |
| # This program is free software: you can redistribute it and/or modify | |
| # it under the terms of the GNU General Public License as published by | |
| # the Free Software Foundation, either version 3 of the License, or | |
| # (at your option) any later version. | |
| # This program is distributed in the hope that it will be useful, |
rjpbonnal
/ gist:2924846
Created
June 13, 2012 15:40
Quick and dirty deployment of your Ruby Gem to your server(s)
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| # You must be the owner of the destination directory | |
| rsync -avz --exclude-from=.gitignore --exclude '.git' -e ssh ./ bioinfoadm@starscream.ingm.ad:/usr/local/lib/ruby/gems/1.9.1/gems/yourgem |
rjpbonnal
/ MultiMemberGZIPInputStream.java
Created
June 11, 2012 19:07
MultiMemberGZIPInputStream Concatenate multiple gzip in java
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| // reference http://bugs.sun.com/bugdatabase/view_bug.do?bug_id=4691425 | |
| // author: I'm not, I could not find he/she but the rights belong to it. | |
| package x.y.z; | |
| import java.io.InputStream; | |
| import java.io.PushbackInputStream; | |
| import java.io.IOException; | |
| public |
rjpbonnal
/ gist:2658172
Created
May 11, 2012 07:36
Parsing Cufflinks Gtf file/data, in an ActiveRecord style
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| g=Bio::Ngs::Cufflinks::Gtf.new "./spec/fixture/transcripts.gtf" | |
| g.set_lazy | |
| a=g.multi_exon.coverage_gt(3).length_gt(200) | |
| #not yet parsed until you iterate of the transcripts | |
| a.multi_exons.each_transcript {|t| puts t; break} | |
| #accessing to an exon using the indexin: | |
| g.read_transcript(10) #return a string of the block | |
| g.get_tranascript(10) #return an object transcript. |
rjpbonnal
/ gist:1315778
Created
October 26, 2011 08:26
CuffDiff output iterator, preliminar example
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| #CLASS DEFINITION Bio::Ngs::Cufflinks | |
| class Diff | |
| include Bio::Command::Wrapper | |
| include Bio::Ngs::Cufflinks::Diff::Utils | |
| set_program Bio::Ngs::Utils.binary("cuffdiff") | |
| add_option "output-dir", :type => :string, :aliases => '-o', :default => "./" | |
| add_option "time-series", :type => :boolean, :aliases => '-T' | |
| add_option "min-alignment-count", :type => :numeric, :aliases => '-c' |
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