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14:21, 15 June 2026 Haars001 talk contribs deleted page Submit job with qsub (content was: "a protocol for submitting using 'qsub'", and the only contributor was "Hjmegens" (talk))
14:20, 15 June 2026 Haars001 talk contribs deleted page Obfuscating runs (content was: "<source lang='bash'> #!/bin/bash #SBATCH --exclusive #SBATCH --nodes=1 #SBATCH --mem=10000 #SBATCH --comment="cv testjob" #SBATCH -p student RND=`< /dev/urandom tr -dc _A-Z-a-z-0-9 | head -c${1:-32};echo;` ln -s `which sleep` $RND echo "Using $RND as binary name" ./$RND 10 </source>", and the only contributor was "Megen002" (talk))
14:20, 15 June 2026 Haars001 talk contribs deleted page Events (content was: "This page contains a list of events of potential interest to the ABGC community. {| class="wikitable" |- ! What? ! When? ! Where? ! Description ! remarks |- | Illumina Sequencing Seminar | Wednesday, December 7, 2011 | Radix Building (Wageningen Campus), room W0.1 | | |- | etc | etc | etc | etc | |- | etc | etc | etc | etc | |}", and the only contributor was "Hjmegens" (talk))
14:20, 15 June 2026 Haars001 talk contribs deleted page List of users (content was: " == Active users == List of users. Alphabetical order (last/family name). Provide some background information by adding information to the 'User:username' page. * Wes Barris (Cobb) * John Bastiaansen (WUR/ABGC) * Rianne van Binsbergen (WUR/ABGC) * Mirte Bosse (WUR/ABGC) * Aniek Bouwman (WUR/ABGC) * Pim Brascamp (WUR/ABGC) * User:Calus001 | Mario Calus (WUR...")
14:19, 15 June 2026 Haars001 talk contribs deleted page Cuda (content was: "CUDA® is a parallel computing platform and programming model invented by NVIDIA. It is a module designed to allow you to write code for NVIDIA graphics processing units (GPUs).", and the only contributor was "Dawes001" (talk))
14:19, 15 June 2026 Haars001 talk contribs deleted page Anunna (content was: "Anunna is a new cluster derived from parts of the HPC AgroGenomics cluster as of January 2019, combined with new infrastructure.", and the only contributor was "Hjmegens" (talk))
14:18, 15 June 2026 Haars001 talk contribs deleted page Manual GitLab (content was: "Manual GitLab@WUR: Create projects and add files == Signing up == If you haven't done so already, install git in your local machine and sign up at GitLab@WUR: https://git.wageningenur.nl == Example of local commands to execute == <source lang='bash'> ## This shows an example, step by step, to create a project and add files into that project. ## Configuration: # 1. Create a folder in your machine, e.g.: mkdir ~/Git_Stuff # 2. configuration step 1: git config --global us...")
07:56, 15 June 2026 User account Strei004 talk contribs was created automatically
09:17, 11 June 2026 Honfi001 talk contribs created page Linux Basic/Linux Self Assessment (Created page with "= Linux Basics — Self-Assessment = This page lets you verify that you have mastered the material from the Linux Basics Course. Work through the parts in order on '''Anunna'''. The final challenge produces a report file that proves you completed every step — submit (or keep) that file as evidence. '''Prerequisites:''' an Anunna account and the course data at <code>/lustre/shared/hpcCourses/shell-lesson-data.zip</code>. '''Rules:''' * Do everything from the comm...")
12:12, 9 June 2026 Haars001 talk contribs deleted page Samtools (content was: "#REDIRECT Samtools v0.1.12a", and the only contributor was "Dawes001" (talk))
12:12, 9 June 2026 Haars001 talk contribs deleted page Installed software (content was: "#REDIRECT Globally_installed_software", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page Downtime (content was: "#REDIRECT Maintenance_and_Management", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page Domain specific software on B4Fcluster installation by users (content was: "#REDIRECT Installation by users", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page Dmtcp (content was: "#REDIRECT Checkpointing", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page DMTCP (content was: "#REDIRECT Checkpointing", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page Checkpoint (content was: "#REDIRECT Checkpointing", and the only contributor was "Vande018" (talk))
12:11, 9 June 2026 Haars001 talk contribs deleted page Agrogenomics Cluster (content was: "#REDIRECT B4F_cluster", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars001 talk contribs deleted page Virtualenv (content was: "#REDIRECT Setting_up_Python_virtualenv", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars001 talk contribs deleted page Trinity (content was: "#REDIRECT Trinity r20131110", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars001 talk contribs deleted page Globally installed software (content was: "== Available as modules == * acml * alphaimpute * bamtools * bcftools * beagle * blacs * blas * BLAST+ * bonnie++ * boost * bowtie * canu * cdo * cmgui * cuda * diamond * dmtcp * emos * fasttree * ferret * ffmpeg * fftw2 * fftw3 * flex * freebayes * gcc * gcta * gdal * gdb * geos * glibc * glimmer * glimmerHMM * globalarrays * grads * grib * gsl * hadoop * hdf4 * hdf5 * hmmer * hpl * htslib *...")
12:10, 9 June 2026 Haars001 talk contribs deleted page Software (content was: "#REDIRECT Globally installed software", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars001 talk contribs deleted page SLURM on B4F cluster (content was: "#REDIRECT Using Slurm", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars001 talk contribs deleted page RAxML (content was: "#REDIRECT RAxML8.0.0", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars001 talk contribs deleted page Log in to B4F cluster (content was: "#REDIRECT Log in to Anunna", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars001 talk contribs deleted page Lustre PFS layout (content was: "#REDIRECT Filesystems", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars001 talk contribs deleted page BCM on B4F cluster (content was: "#REDIRECT BCM on Anunna", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars001 talk contribs deleted page Installation by users (content was: "== Domain specific folders for executables and libraries == Many packages and applications can be installed locally in the $HOME directory. Users of each of the groups (e.g. 'WUR/ABGC') can deposit a map with executables or library files that can be of interest to multiple users /cm/shared/apps/WUR/ABGC/ == Preparing modules for local or domain specific use == Example of making a very simple module that would load a specific version of the short-read aligner bwa to your e...")
12:07, 9 June 2026 Haars001 talk contribs deleted page Hmmer (content was: "#REDIRECT Hmmer_3.1", and the only contributor was "Dawes001" (talk))
12:07, 9 June 2026 Haars001 talk contribs deleted page Whole genome alignment pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG For up-to-date documentation see [https://github.com/CarolinaPB/whole-genome-alignment here] = Whole genome alignment pipeline = Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/whole-genome-alignment == First follow the instructions here: == [https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by st...")
12:06, 9 June 2026 Haars001 talk contribs deleted page Single Cell preprocessing pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG For up-to-date documentation see [https://github.com/CarolinaPB/single-cell-data-processing here] = Single Cell preprocessing pipeline = Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/single-cell-data-processing =...", and the only contributor was "Moiti001" (talk))
12:06, 9 June 2026 Haars001 talk contribs deleted page Population variant calling pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG For up-to-date documentation see [https://github.com/CarolinaPB/population-variant-calling here] = Population level variant calling = Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/population-variant-calling == First follow the instructions here == [https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Ste...")
12:06, 9 June 2026 Haars001 talk contribs deleted page Nanopore assembly and variant calling (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG For up-to-date documentation see [https://github.com/CarolinaPB/nanopore-assembly here] = Assemble nanopore reads and do variant calling with short and long reads = Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/nanopore-assembly == First follow the instructions here:...", and the only contributor was "Moiti001" (talk))
12:06, 9 June 2026 Haars001 talk contribs deleted page Population mapping pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG [https://github.com/CarolinaPB/population-mapping Link to the repository] == First follow the instructions here: == [https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by step guide on how to use my pipelines] Click [https://github.com/CarolinaPB/snakemake-...", and the only contributor was "Moiti001" (talk))
12:06, 9 June 2026 Haars001 talk contribs deleted page Population structural variant calling pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG [https://github.com/CarolinaPB/population-structural-var-calling-smoove/tree/single_run Link to the repository] == First follow the instructions here: == [https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ Step by step guide on how to use my pipelines] Click [https://github.com/CarolinaPB/snakemake-template/blob/master/Short%20introduction%20to%20Snakemake.pdf here...")
12:06, 9 June 2026 Haars001 talk contribs deleted page Mapping and variant calling pipeline (content was: "Author: Carolina Pita Barros Contact: carolina.pitabarros@wur.nl ABG Path to pipeline: /lustre/nobackup/WUR/ABGC/shared/PIPELINES/mapping-variant-calling [https://github.com/CarolinaPB/WUR_mapping-variant-calling Link to the repository] == First follow the instructions here: == [https://carolinapb.github.io/2021-06-23-how-to-run-my-pipelines/ St...", and the only contributor was "Moiti001" (talk))
12:06, 9 June 2026 User account Lucht004 talk contribs was created automatically
12:05, 9 June 2026 Haars001 talk contribs deleted page Bioinformatics tips tricks workflows (content was: "This page is intended as a portal to pages concerning best practices, workflows and pipelines, and other protocols (including scripts). == A list of tutorials, workflows, and recipes == * Mapping Illumina GA2/HiSeq reads to the Sus scrofa genome assembly * A Perl script to convert fastq to fasta file format * Mapping Pair-end reads with Stampy * making_slices_from_BAM_files | Create slices from a collection of...")
12:05, 9 June 2026 Haars001 talk contribs deleted page Bowtie2 (content was: "#REDIRECT Bowtie2_v2.2.1", and the only contributor was "Dawes001" (talk))
11:18, 8 June 2026 Lee006 talk contribs created page File:Image.png
11:18, 8 June 2026 Lee006 talk contribs uploaded File:Image.png
13:27, 29 May 2026 Haars001 talk contribs deleted page Wgs assembler 8.1 (content was: "[http://sourceforge.net/apps/mediawiki/wgs-assembler/index.php?title=Main_Page Celera Assembler] is a de novo whole-genome shotgun (WGS) DNA sequence assembler. It reconstructs long sequences of genomic DNA from fragmentary data produced by whole-genome shotgun sequencing. Celera Assembler has enabled many advances in genomics, including the first whole genome shotgun seque...", and the only contributor was "Megen002" (talk))
13:27, 29 May 2026 Haars001 talk contribs deleted page Trinity r20131110 (content was: "'''[http://trinityrnaseq.sourceforge.net/#running_trinity Trinity]''', developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity partitions the sequence data into many individual de Bruijn gr...")
13:27, 29 May 2026 Haars001 talk contribs deleted page TopHat 2.0.11 (content was: "'''[http://tophat.cbcb.umd.edu TopHat]''' is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. == Module file == The module file can be found in this location: /cm/shared/modulefile...", and the only contributor was "Megen002" (talk))
13:27, 29 May 2026 Haars001 talk contribs deleted page Sra toolkit 2.3.4 (content was: "[http://eutils.ncbi.nih.gov/Traces/sra/sra.cgi?view=announcement The Sequence Read Archive (SRA)] stores raw sequence data from "next-generation" sequencing technologies including 454, IonTorrent, Illumina, SOLiD, Helicos and Complete Genomics. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. SRA...", and the only contributor was "Megen002" (talk))
13:26, 29 May 2026 Haars001 talk contribs deleted page Soapdenovo2 r240 (content was: " '''[http://soap.genomics.org.cn/soapdenovo.html#intro2 SOAPdenovo2]''' is a popular genome assembler. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <source lang='tcl'>#%Module1.0####################################################################### ## SOAPdenovo2 r240 modulefile ## proc ModulesHelp { } { puts...", and the only contributor was "Megen002" (talk))
13:26, 29 May 2026 Haars001 talk contribs deleted page Snap (content was: "SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## snap 2013-11-29 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds snap 2013-11-29 to your environment" } module-w...")
13:26, 29 May 2026 Haars001 talk contribs deleted page Services (content was: "Several additional services are also attached to Anunna's environment: * [https://wiki.anunna.wur.nl This wiki] is what you're looking at now. * [https://galaxy.anunna.wur.nl Galaxy] is a point-and-click friendly way of running genomics pipelines, which offloads the workload onto Anunna. * [https://notebook.anunna.wur.nl Jupyterhub] , the Jupyter notebook server, is a web-accessible environment for many languages. Primarily Python, includes R, octave, Julia etc.")
13:25, 29 May 2026 Haars001 talk contribs deleted page Samtools v0.1.19 (content was: "[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## samtools 0.1.19 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds sa...")
13:25, 29 May 2026 Haars001 talk contribs deleted page Samtools v0.1.12a (content was: "[http://samtools.sourceforge.net SAM Tools] provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## samtools 0.1.12a modulefile ## proc ModulesHelp { } { puts stderr "\tAdds s...")
13:25, 29 May 2026 Haars001 talk contribs deleted page SLURM Compare (content was: "=== Rosetta Stone of Workload Managers === PBS/Torque, Slurm, LSF, SGE and LoadLeveler [http://slurm.schedmd.com/rosetta.html Rosetta Stone] This table lists the most common command, environment variables, and job specification options used by the major workload management systems: PBS/Torque, Slurm, LSF, SGE and LoadLeveler. Each of these workload managers has unique features, but the most commonly used functionality is available in all of these environments as listed in the...")

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