Deletion log

Below is a list of the most recent deletions.

12:12, 9 June 2026 Haars0011 talk contribs deleted page Samtools (content was: "#REDIRECT Samtools v0.1.12a", and the only contributor was "Dawes001" (talk))
12:12, 9 June 2026 Haars0011 talk contribs deleted page Installed software (content was: "#REDIRECT Globally_installed_software", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars0011 talk contribs deleted page Downtime (content was: "#REDIRECT Maintenance_and_Management", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars0011 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 Haars0011 talk contribs deleted page Dmtcp (content was: "#REDIRECT Checkpointing", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars0011 talk contribs deleted page DMTCP (content was: "#REDIRECT Checkpointing", and the only contributor was "Dawes001" (talk))
12:11, 9 June 2026 Haars0011 talk contribs deleted page Checkpoint (content was: "#REDIRECT Checkpointing", and the only contributor was "Vande018" (talk))
12:11, 9 June 2026 Haars0011 talk contribs deleted page Agrogenomics Cluster (content was: "#REDIRECT B4F_cluster", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars0011 talk contribs deleted page Virtualenv (content was: "#REDIRECT Setting_up_Python_virtualenv", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars0011 talk contribs deleted page Trinity (content was: "#REDIRECT Trinity r20131110", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars0011 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 Haars0011 talk contribs deleted page Software (content was: "#REDIRECT Globally installed software", and the only contributor was "Dawes001" (talk))
12:10, 9 June 2026 Haars0011 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 Haars0011 talk contribs deleted page RAxML (content was: "#REDIRECT RAxML8.0.0", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars0011 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 Haars0011 talk contribs deleted page Lustre PFS layout (content was: "#REDIRECT Filesystems", and the only contributor was "Dawes001" (talk))
12:09, 9 June 2026 Haars0011 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 Haars0011 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 Haars0011 talk contribs deleted page Hmmer (content was: "#REDIRECT Hmmer_3.1", and the only contributor was "Dawes001" (talk))
12:07, 9 June 2026 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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))
12:05, 9 June 2026 Haars0011 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 Haars0011 talk contribs deleted page Bowtie2 (content was: "#REDIRECT Bowtie2_v2.2.1", and the only contributor was "Dawes001" (talk))
13:27, 29 May 2026 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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 Haars0011 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...")
13:25, 29 May 2026 Haars0011 talk contribs deleted page RepeatModeler 1.0.7 (content was: "[http://www.repeatmasker.org/RepeatModeler.html RepeatModeler] is a de-novo repeat family identification and modeling package. At the heart of RepeatModeler are two de-novo repeat finding programs ( RECON and RepeatScout ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data. RepeatModeler assists in automating the runs of RECON and RepeatScout given a genomic database and uses the output to build...")
13:24, 29 May 2026 Haars0011 talk contribs deleted page RepeatMasker 4.0.3 (content was: "[http://www.repeatmasker.org RepeatMasker]RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (i.e. replace...", and the only contributor was "Megen002" (talk))
13:24, 29 May 2026 Haars0011 talk contribs deleted page RAxML8.0.0 (content was: "'''[http://www.exelixis-lab.org RAxML]''' (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It can also be used for postanalyses of sets of phylogenetic trees, analyses of alignments and, evolutionary placement of short reads. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0########################################...")
13:24, 29 May 2026 Haars0011 talk contribs deleted page Quantitative genetics protocols ABG Chairgroup (content was: "* run_ASREML_with_SGE", and the only contributor was "Hjmegens" (talk))
13:24, 29 May 2026 Haars0011 talk contribs deleted page Quantitative genetics (content was: "* Quantitative genetics Discussion Group: QDG * Quantitative genetics: topics * best practices, tips and workflows", and the only contributor was "Hjmegens" (talk))
13:24, 29 May 2026 Haars0011 talk contribs deleted page Provean Sus scrofa (content was: "This page describes the procedure for mapping all known variants (batch of first 150 pigs, wild boar re-sequencing) at the ABGC. == Pre-requisites == From Variant Effect Predictor output, select only protein altering variants and sort by transcript: <source lang='bash'> cat outVEP_*.txt | awk '$11~/\//' | sed 's/:/\t/' | sort -k6 >prot_alt.txt </source> Protein models for Sus scrofa: /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/pig/Ensembl74/pep/Sus_scrofa.Ss...")
13:23, 29 May 2026 Haars0011 talk contribs deleted page Provean 1.1.3 (content was: "[http://provean.jcvi.org/about.php PROVEAN] was developed to predict whether a protein sequence variation affects protein function. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## Provean 1.1.3 modulefile ## proc ModulesHelp { } { puts stderr "\tAdds Provean 1.1.3 to your environment" } module-whatis "Adds Provean 1.1.3 to y...")
13:23, 29 May 2026 Haars0011 talk contribs deleted page Plink 1.9 (content was: "[https://www.cog-genomics.org/plink2/ PLINK] is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. Development of the baseline PLINK toolset has resumed and beta testing for the next (1.90) release has now begun.The new release, by Chris Chang and colleagues, is a complete rewrite of the original code and represents a very significant improvement in overall speed and fu...")
13:23, 29 May 2026 Haars0011 talk contribs deleted page Plink 1.07 (content was: "[http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml PLINK] is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. == Module file == The module file can be found in this location: /cm/shared/modulefiles/SHARED/ <pre> #%Module1.0####################################################################### ## plink 1.07 modulefile ## proc ModulesHelp { } { puts s...")
13:22, 29 May 2026 Haars0011 talk contribs deleted page Muscle 3.8.31 (content was: "'''[http://www.drive5.com/muscle/ MUSCLE]''' is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line optio...", and the only contributor was "Megen002" (talk))
13:22, 29 May 2026 Haars0011 talk contribs deleted page Migration from ESG HPC (content was: " == Folders == home folder (200GB limit): /home/WUR/<user>/ lustre backup folder: /lustre/backup/WUR/ESG/<user>/ lustre no-backup folder: /lustre/nobackup/WUR/ESG/<user>/ /DATA folder /lustre/backup/WUR/ESG/data/ == Example of a job script == #!/bin/bash #SBATCH --comment=99999999 #SBATCH --time=1200 #SBATCH --mem=2048 #SBATCH --ntasks=1 #SBATCH --output=output_%j.txt #SBATCH --error=error_output_%j.txt #SBATCH --job-name="test slurm" #SBATCH --no...")
13:20, 29 May 2026 Haars0011 talk contribs deleted page Maker protocols Pmajor (content was: "This page describes the various rounds of [http://www.yandell-lab.org/software/maker.html Maker]-based annotations for the [http://en.wikipedia.org/wiki/Parus_major ''Parus major'' (Great Tit)] genome. == Round 1 == === Rationale === For this round no P. major-based ESTs were available. Zebrafinch (T. guttata) is the closest relative for which a reasonably complete gene-model set is available. As a first pass, it was decided to let gene predictions be driven by ab-inititio pr...")

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