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NEWS
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@ -142,10 +142,6 @@
adaptive methods
https://link.springer.com/article/10.1134/S0016793217010108
* GNU Parallel was cited in: Proper experimental design requires
randomization/balancing of molecular ecology experiments
http://biorxiv.org/content/biorxiv/early/2017/02/17/109280.full.pdf
* GNU Parallel was cited in: Higher likelihood of multiple bit-flips
due to neutron-induced strikes on logic gates
https://arxiv.org/pdf/1612.08239.pdf
@ -162,11 +158,6 @@
Theory for Many External Particles
https://arxiv.org/pdf/1611.08003.pdf
* GNU Parallel was cited in: Large-scale benchmarking reveals false
discoveries and count transformation sensitivity in 16S rRNA gene
amplicon data analysis methods used in microbiome studies
https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-016-0208-8
* GNU Parallel was cited in: Operations Research Applications in
Nuclear Energy
https://dspace.library.colostate.edu/bitstream/handle/11124/170687/Johnson_mines_0052E_11207.pdf?sequence=1&isAllowed=y
@ -218,12 +209,6 @@
gout, and the apple genome
https://ourarchive.otago.ac.nz/bitstream/handle/10523/7060/BoocockJames2016MSc.pdf?sequence=3
* GNU Parallel was cited in: Determination of crystal structures of
proteins of unknown identity using a marathon molecular replacement
procedure: structure of Stenotrophomonas maltophilia
phosphate-binding protein
https://www.researchgate.net/publication/308186413_Determination_of_crystal_structures_of_proteins_of_unknown_identity_using_a_marathon_molecular_replacement_procedure_Structure_of_Stenotrophomonas_maltophilia_phosphate-binding_protein
* GNU Parallel was cited in: Reaction rates for reaction-diffusion
kinetics on unstructured meshes
http://aip.scitation.org/doi/10.1063/1.4975167
@ -333,24 +318,12 @@
transcript-expression levels in public cancer compendia
http://www.nature.com/articles/srep39259
* GNU Parallel was cited in: Learning string distance with smoothing
for OCR spelling correction
http://paperity.org/p/78557440/learning-string-distance-with-smoothing-for-ocr-spelling-correction
* GNU Parallel was cited in: Transient compute clustering with GNU
Parallel and sshfs
https://gist.github.com/Brainiarc7/24c966c8a001061ee86cc4bc05826bf4
* GNU Parallel was cited in: Determination of crystal structures of
proteins of unknown identity using a marathon molecular replacement
procedure: Structure of Stenotrophomonas maltophilia
phosphate-binding protein
https://www.researchgate.net/publication/308186413_Determination_of_crystal_structures_of_proteins_of_unknown_identity_using_a_marathon_molecular_replacement_procedure_Structure_of_Stenotrophomonas_maltophilia_phosphate-binding_protein
* GNU Parallel was cited in: The Outer Solar System Origins Survey:
I. Design and First-Quarter Discoveries
https://arxiv.org/pdf/1511.02895v2.pdf
* GNU Parallel was cited in: Large-scale benchmarking reveals false
discoveries and count transformation sensitivity in 16S rRNA gene
amplicon data analysis methods used in microbiome studies
@ -360,6 +333,9 @@
RGB-space Geometry
https://cs.gmu.edu/~ygingold/singleimage/Decomposing%20Images%20into%20Layers%20via%20RGB-space%20Geometry%20(Tan%20et%20al%202016%20TOG)%20small.pdf
* Transient compute clustering with GNU Parallel and sshfs
https://gist.github.com/Brainiarc7/24c966c8a001061ee86cc4bc05826bf4
* 4 Ways to Batch Convert Your PNG to JPG and Vice-Versa
http://www.tecmint.com/linux-image-conversion-tools/
@ -434,9 +410,6 @@
approach: IRMA, the iterative refinement meta-assembler
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5011931/
* GNU Parallel is used in Gene Set Omic Analysis:
https://bitbucket.org/srp33/gsoa
* Using GNU Parallel and ImageMagick for Conversions
https://blog.fractalcomic.com/tutorials/using-gnu-parallel-and-imagemagick-for-conversions/
@ -528,10 +501,6 @@
correlation analysis of genomic data
http://biorxiv.org/content/biorxiv/suppl/2016/04/06/047217.DC1/047217-1.pdf
* GNU Parallel was cited in: Computational Design of DNA-Binding
Proteins
http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
* GNU Parallel was cited in: Math Indexer and Searcher under the Hood:
Fine-tuning Query Expansion and Unification Strategies
http://research.nii.ac.jp/ntcir/workshop/OnlineProceedings12/pdf/ntcir/MathIR/05-NTCIR12-MathIR-RuzickaM.pdf
@ -630,7 +599,7 @@
http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=7407131
* GNU Parallel was cited in: Oops, my tests broke the build: An
analysis of Travis CI buildswith GitHub
analysis of Travis CI builds with GitHub
https://peerj.com/preprints/1984/
* GNU Parallel was cited in: Drosophila Muller F Elements Maintain a
@ -642,10 +611,6 @@
Environments
http://biorxiv.org/content/biorxiv/early/2016/03/24/022707.full.pdf
* GNU Parallel was cited in: Functional enrichments of disease
variants across thousands of independent loci in eight diseases
http://biorxiv.org/content/early/2016/04/11/048066.abstract
* GNU Parallel was cited in: PleaseTM: Enabling Transaction Conflict
Management in Requester-wins Hardware Transactional Memory
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7446072
@ -669,10 +634,6 @@
https://dl.acm.org/citation.cfm?id=2884799 (It has the cutest
thumbnail graphs I have ever seen scattered all over the text)
* GNU Parallel was cited in: StrAuto: Automation and Parallelization
of STRUCTURE Analysis
http://vchhatre.w3.uvm.edu/download/strauto/strauto_doc.pdf
* GNU Parallel was cited in: Data processing pipeline for serial
femtosecond crystallography at SACLA
http://journals.iucr.org/j/issues/2016/03/00/zw5001/index.html
@ -680,14 +641,6 @@
* GNU Parallel was cited in: Reconstruction of Fine-Scale Auroral
Dynamics http://arxiv.org/pdf/1512.01460.pdf
* GNU Parallel was cited in: The Outer Solar System Origins Survey:
I. Design and First-Quarter Discoveries
http://arxiv.org/pdf/1511.02895.pdf
* GNU Parallel was cited in: Multiscale Estimation of Binding Kinetics
Using Brownian Dynamics, Molecular Dynamics and Milestoning
http://journals.plos.org/ploscompbiol/article/asset?id=10.1371%2Fjournal.pcbi.1004381.PDF
* GNU Parallel was cited in: Genomic legacy of the African cheetah,
Acinonyx jubatus
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4676127/pdf/13059_2015_Article_837.pdf
@ -701,10 +654,6 @@
Genomics, Transcriptomics and Proteogenomics
http://journals.plos.org/plosone/article/asset?id=10.1371%2Fjournal.pone.0147221.PDF
* GNU Parallel was cited in: Stride Search: a general algorithm for
storm detection in high-resolution climate data
http://www.geosci-model-dev-discuss.net/8/7727/2015/gmdd-8-7727-2015.pdf
* GNU Parallel was cited in: How attention influences perceptual
decision making: Single-trial EEG correlates of drift-diffusion
model parameters http://www.cidlab.com/prints/nunez2016attention.pdf
@ -740,10 +689,6 @@
Australian Aboriginal population for health-based research
http://www.nature.com/articles/sdata201623
* GNU Parallel was cited in: Computational Design of DNA-Binding
Proteins
http://link.springer.com/protocol/10.1007/978-1-4939-3569-7_16
* GNU Parallel was cited in: Do aye-ayes echolocate?
http://biorxiv.org/content/biorxiv/early/2016/04/11/048165.full.pdf
@ -792,18 +737,10 @@
* Better CPU detection on OpenIndiana.
* GNU Parallel was cited in: How Can We Measure the Similarity Between
Resumes of Selected Candidates for a Job?
https://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_resumes_of_selected_candidates_for_a_job
* GNU Parallel was cited in: Automatic Methods for Assisted
Recruitment
https://www.researchgate.net/publication/297738658_Automatic_Methods_for_Assisted_Recruitment
* GNU Parallel was cited in: Tools and techniques for computational
reproducibility
http://biorxiv.org/content/biorxiv/early/2016/03/17/022707.full.pdf
* GNU Parallel was cited in: Reinterpretation of ATLAS 8 TeV searches
for Natural SUSY with a R-Sneutrino LSP
http://arxiv.org/pdf/1603.06130.pdf
@ -815,9 +752,6 @@
* A basic demo of how GNU Parallel can speed up execution of commands
https://www.youtube.com/watch?v=kl8LO2jcvMc
* Downloading a list of URLs
http://blog.gypsydave5.com/2016/02/04/xargs-and-curl/
* qbatch uses GNU Parallel: https://pypi.python.org/pypi/qbatch/1.0rc2
* FaceCrop uses GNU Parallel: https://github.com/EderSantana/FaceCrop
@ -954,15 +888,6 @@
Environments
http://research.gold.ac.uk/15078/1/COM_thesis_JonesD_2015.pdf
* GNU Parallel was cited in: Contrasting genetic architectures of
schizophrenia and other complex diseases using fast
variance-components analysis
http://www.nature.com/ng/journal/v47/n12/full/ng.3431.html
* GNU Parallel was cited in: Efficient Retrieval of Key Material for
Inspecting Potentially Malicious Traffic in the Cloud
http://www.cs.bham.ac.uk/~bxb/Papres/2015.1.pdf
* GNU Parallel was cited in: Achieving Consistent Doppler Measurements
from SDO/HMI Vector Field Inversions
http://arxiv.org/pdf/1511.06500.pdf
@ -1054,9 +979,6 @@
* GNU Parallel is used in TraitAR:
https://testpypi.python.org/pypi/traitar/0.1.4
* GNU Parallel is used in youtube-dl-parallel:
https://github.com/dlh/youtube-dl-parallel
* A parallel and fast way to download multiple files
http://onetipperday.blogspot.com/2015/10/a-parallel-and-fast-way-to-download.html
@ -1075,22 +997,13 @@
* GNU Parallel was cited in: BL1: 2D Potts Model with a Twist
https://sucs.swan.ac.uk/~rjames93/Dissertation.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic
Platform Bridging the Gap between the Robust Validation of Docking
Protocols and Virtual Screening Simulations
http://www.mdpi.com/1420-3049/20/6/9977/pdf
* GNU Parallel was cited in: A Scalable Parallel Implementation of
Evolutionary Algorithms for Multi-Objective Optimization on GPUs
http://ieeexplore.ieee.org/stamp/stamp.jsp?tp=&arnumber=7257074
* GNU Parallel was cited in: Tools and techniques for computational
reproducibility
http://biorxiv.org/content/biorxiv/early/2015/07/17/022707.full.pdf
* GNU Parallel was cited in: How Can We Measure the Similarity Between
Résumés of Selected Candidates for a Job?
http://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_rsums_of_selected_candidates_for_a_job
https://www.researchgate.net/publication/275954089_How_can_we_measure_the_similarity_between_rsums_of_selected_candidates_for_a_job
* GNU Parallel was cited in: Interplay of cell dynamics and epithelial
tension during morphogenesis of the Drosophila pupal wing
@ -1124,10 +1037,6 @@
* Version of GNU Parallel that uses PostgreSQL as backend
https://github.com/stephen-fralich/parallel-sql/
* A composite genome approach to identify phylogenetically informative
data from next-generation sequencing
http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
* SpeedSeq: ultra-fast personal genome analysis and interpretation
http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.3505.html
@ -1181,10 +1090,6 @@
* GNU Parallel was cited in: A Fast Compiler for NetKAT
http://arxiv.org/pdf/1506.06378.pdf
* GNU Parallel was cited in: Flexible Modeling of Epidemics with an
Empirical Bayes Framework
http://www.stat.cmu.edu/~ryantibs/papers/empbayes.pdf
* GNU Parallel was cited in: Decomposing Time-Lapse Paintings into
Layers
http://cs.gmu.edu/~ygingold/timemap/Decomposing%20Time-Lapse%20Paintings%20into%20Layers%20(Tan%20et%20al%202015%20SIGGRAPH)%20600dpi.pdf
@ -1238,11 +1143,6 @@
* Q(...) can be used in {= =} to shell quote a string.
* GNU Parallel was cited in: Contrasting regional architectures of
schizophrenia and other complex diseases using fast variance
components analysis
http://biorxiv.org/content/biorxiv/early/2015/06/05/016527.full.pdf
* GNU Parallel was cited in: DockBench: An Integrated Informatic
Platform Bridging the Gap between the Robust Validation of Docking
Protocols and Virtual Screening Simulations
@ -1264,10 +1164,6 @@
phylogenetically informative data from next-generation sequencing
http://www.biomedcentral.com/content/pdf/s12859-015-0632-y.pdf
* GNU Parallel was cited in: Tutorial: Lorenz-Mie theory for 2D
scattering and resonance calculations
http://arxiv.org/pdf/1505.07691.pdf
* GNU Parallel is used in: taxator-tk
http://algbio.cs.uni-duesseldorf.de/webapps/wa-download/
@ -1306,10 +1202,6 @@
Metagenomics and RNA-seq
http://biorxiv.org/content/biorxiv/early/2015/05/05/018085.full.pdf
* GNU Parallel was cited in: Toward Enhanced Metadata Quality of
Large-Scale Digital Libraries: Estimating Volume Time Range
https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
* GNU Parallel was cited in: Sequencing the cap-snatching repertoire
of H1N1 influenza provides insight into the mechanism of viral
transcription initiation
@ -1319,11 +1211,6 @@
long and error-free DNA reads
http://www.biomedcentral.com/content/pdf/s12864-015-1519-z.pdf
* GNU Parallel was cited in: Contrasting regional architectures of
schizophrenia and other complex diseases using fast variance
components analysis
http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
* GNU Parallel was used (unfortunately with wrong citation) in:
Comparing the CarbonTracker and TM5-4DVar data assimilation systems
for CO2 surface flux inversions
@ -1351,9 +1238,6 @@
* Importing huge databases faster
https://www.lullabot.com/blog/article/importing-huge-databases-faster
* Run multiple ssh commands in parallel with GNU Parallel
https://www.ameir.net/blog/archives/380-run-multiple-ssh-commands-in-parallel-with-gnu-parallel.html/comment-page-1
* Parallel? Gnu parallel! https://debian.pro/1834
* Bug fixes and man page updates.
@ -1386,11 +1270,6 @@ New in this release:
Large-Scale Digital Libraries: Estimating Volume Time Range
https://www.ideals.illinois.edu/bitstream/handle/2142/73656/186_ready.pdf
* GNU Parallel was cited in: Contrasting regional architectures of
schizophrenia and other complex diseases using fast variance
components analysis
http://biorxiv.org/content/biorxiv/early/2015/03/13/016527.full.pdf
* GNU Parallel was cited in: Experimental study on the Wind Farm
Substation Cable Installation Problem
http://i11www.iti.uni-karlsruhe.de/_media/teaching/theses/ma-schmitz-14.pdf
@ -1425,9 +1304,6 @@ New in this release:
* Add an ENVI header to JAXA Global Mangrove Watch PALSAR tiles
https://spectraldifferences.wordpress.com/2015/03/24/add-an-envi-header-to-jaxa-global-mangrove-watch-palsar-tiles/
* GNU Parallel (Sebuah Uji Coba)
http://kaka.prakasa.my.id/2014/09/04/gnu-parallel-sebuah-uji-coba/
* 你见过的最牛逼的命令行程序是什么？
http://www.zhihu.com/question/29257300
@ -1549,10 +1425,6 @@ New in this release:
Analysis of Big Data from Mars: A Noachis Terra Case Study
http://link.springer.com/chapter/10.1007/978-3-319-13865-7_25
* GNU Parallel was cited in: Towards Recommender Engineering Tools and
Experiments for Identifying Recommender Differences
http://elehack.net/research/thesis/mde-thesis.pdf
* GNU Parallel was used (unfortunately with wrong citation) in:
Performance and Scaling Comparison Study of RDBMS and NoSQL
(MongoDB)
@ -1610,10 +1482,6 @@ New in this release:
* A bug fix in replacement strings caused rewrite of the replacement
function. This makes use of replacement strings alpha quality.
* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for
the Histological Quantification of Whole Slide Images
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289
* GNU Parallel was cited in: Improving Energy and Performance with
Spintronics Caches in Multicore Systems
http://link.springer.com/chapter/10.1007/978-3-319-14313-2_24
@ -1638,9 +1506,6 @@ New in this release:
* GNU Parallel was cited in: Clonal interference and Mullerʼs ratchet
in spatial habitats http://iopscience.iop.org/1478-3975/11/5/056003
* GNU Parallel was cited in: Web-scale content reuse detection
ftp://info.isi.edu/isi-pubs/tr-692.pdf
* GNU Parallel was cited in: Computação Verde na Camada de Aplicação
https://linux.ime.usp.br/~tpaiva/mac0499/files/monografia.pdf
@ -1734,7 +1599,7 @@ New in this release:
* GNU Parallel was cited in: SlideToolkit: An Assistive Toolset for
the Histological Quantification of Whole Slide Images
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289#close
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0110289
* GNU Parallel was cited in: Exploring a multiprocessor design space
to analyze the impact of using STT-RAM in the memory hierarchy
@ -1786,9 +1651,6 @@ New in this release:
* Comparing Golang, Scala, Elixir and Ruby for ETL
http://www.dimroc.com/2014/09/29/etl-language-showdown/
* Parallelizing Batch Jobs for Fun and Profit
http://mikeseidle.com/tech/programming/2013/03/parallelizing-batch-jobs
* Assemble a list of which of these hosts are up or down
http://opsfun.wordpress.com/2014/03/31/gnu-parallel/
@ -2471,9 +2333,6 @@ New in this release:
* Compression of files in parallel using GNU parallel
http://codextechnicanum.blogspot.dk/2013/07/compression-of-files-in-parallel-using.html
* Using GNU Parallel to roll-your-own Map Reduce!
http://www.rankfocus.com/?p=1
* Using GNU Parallel with Amazon
media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf
@ -2868,12 +2727,6 @@ New in this release:
* Blog post: Running commands in parallel using bash.
http://blog.michaelboman.org/2012/04/running-commands-in-parallel-using-bash.html
* Blog post: Efficient log processing.
http://www.francoismaillet.com/blog/?p=399
* Blog post about GNU Parallel and Amazon EC2.
http://blog.kevinformatics.com/post/4970574713/interested-in-your-experience-using-gnu-parallel-in
* Blog post in Hungarian.
http://commandline.blog.hu/2012/05/03/gnu_parallel
@ -3050,9 +2903,6 @@ New in this release:
* Blog post on using GNU Parallel of Mac OS X.
http://www.0xcb0.com/2011/10/19/running-parallel-bash-tasks-on-os-x/
* Blog post in English about using zip with GNU Parallel.
http://nuclear-imaging.info/site_content/2011/05/11/gnu-parallel/
* Blog post in English by researcher.
http://zandyware.wordpress.com/2011/10/15/gnu-parallell-make-best-use-of-your-multicore-computer/
@ -3352,9 +3202,6 @@ New in this release:
* Using GNU Parallel instead of xargs. Thanks to James Cuff.
http://blog.jcuff.net/2011/02/on-train-ride-in.html
* Using GNU Parallel from 0install (German). Thanks to AdaMin.
http://forum.ubuntuusers.de/topic/gnu-parallel-mit-zero-install-kurzinfo-kein-wi/
* Bug fixes and man page updates.

67
doc/release_new_version
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@ -174,8 +174,8 @@ http://freshmeat.net/projects/parallel/releases/new
https://joindiaspora.com/stream
New release of #GNU Parallel pi․dk/0 New in this release pi․dk/2 See the intro videos pi․dk/1
10 secs installation: wget -O - pi․dk/3|bash
New release of #GNU Parallel pi.dk/0 New in this release pi.dk/2 See the intro videos pi.dk/1
10 secs installation: wget -O - pi.dk/3|bash
[x] Twitter
Aspect: Public
@ -196,82 +196,55 @@ file:///home/tange/privat/parallel/doc/release_new_version
from:tange@gnu.org
to:parallel@gnu.org, bug-parallel@gnu.org
Subject: GNU Parallel 20170522 ('Macron') released [stable]
Subject: GNU Parallel 20170622 ('Manchester') released <<[stable]>>
GNU Parallel 20170522 ('Macron') [stable] has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
GNU Parallel 20170622 ('Manchester') <<[stable]>> has been released. It is available for download at: http://ftpmirror.gnu.org/parallel/
Very little new functionality was introduced so this is a good candidate for a stable release.>>
<<No new functionality was introduced so this is a good candidate for a stable release.>>
Haiku of the month:
Always test your script
using a --dry-run
or --dr
<<>>
-- Ole Tange
New in this release:
* --timeout can now use s=second,m=minute,h=hour,d=day.
* Vote for GNU Parallel's community ads on
http://meta.unix.stackexchange.com/a/4356/2972
http://meta.askubuntu.com/a/16750/22307
http://meta.serverfault.com/a/9040/45704
* --dr is now an alias for --dry-run.
* Graph for overhead for 1000 jobs has been updated. It remains steadily at 3.5 ms per job on a 1.7 GHz machine https://www.gnu.org/software/parallel/process-time-j2-1700MHz-3000-1000.pdf
* Vote for GNU Parallel's community ads on http://meta.unix.stackexchange.com/a/4356/2972 http://meta.askubuntu.com/a/16750/22307 http://meta.serverfault.com/a/9040/45704
* GNU Parallel was cited in: The topology of the directed clique complex as a network invariant https://springerplus.springeropen.com/articles/10.1186/s40064-016-2022-y
* GNU Parallel was cited in: Feature Detection in Visual Cortex during Different Functional States https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5397493/
* GNU Parallel was cited in:
* GNU Parallel was cited in: From genotype to phenotype: inferring relationships between microbial traits and genomic components https://docserv.uni-duesseldorf.de/servlets/DerivateServlet/Derivate-44622/main.pdf
https://support.ehelp.edu.au/support/solutions/articles/6000089713-tips-for-running-jobs-on-your-vm#parallel
* GNU Parallel was cited in: Designing fecal microbiota transplant trials that account for differences in donor stool efficacy http://biorxiv.org/content/biorxiv/early/2016/07/25/065383.full.pdf
<<Citation not OK: BAMClipper: removing primers from alignments to minimize false-negative mutations in amplicon next-generation sequencing https://www.nature.com/articles/s41598-017-01703-6>>
* GNU Parallel was cited in: Assessing the predictability of anharmonic vibrational modes at the example of hydroxyl groups - ad hoc construction of localised modes and the influence of structural solute–solvent motifs http://pubs.rsc.org/-/content/articlelanding/2017/cp/c7cp01662j#!divAbstract
<<Wrong citation https://iris.sissa.it/retrieve/handle/20.500.11767/36149/10823/And%C3%B2_tesi.pdf>>
* GNU Parallel was cited in: Mapping Environmental Influences on Utility Fire Threat ftp://frapftp.fire.ca.gov/outgoing/transfer/PUC_Map1/Utility%20Fire%20map%201%20final%20review%20and%20development%20report21616.pdf
* GNU Parallel was cited in: Weak vs. Strong Disorder Superfluid-Bose Glass Transition in One Dimension https://arxiv.org/pdf/1704.02257.pdf
* GNU Parallel was cited in: Online Automatic Post-editing for MT in a Multi-Domain Translation Environment https://www.aclweb.org/anthology/E/E17/E17-1050.pdf
* GNU Parallel was cited in: Cross-calibration of S-NPP VIIRS moderate-resolution reflective solar bands against MODIS Aqua over dark water scenes http://www.atmos-meas-tech.net/10/1425/2017/amt-10-1425-2017.pdf
* GNU Parallel was cited in: Scattering Networks: Efficient 2D Implementation And Application To Melanoma Classification http://amslaurea.unibo.it/12261/1/nurrito_eugenio_tesi_fisica_magistrale.pdf
* GNU Parallel was cited in: Genome-scale detection of positive selection in 9 primates predicts human-virus evolutionary conflicts http://biorxiv.org/content/biorxiv/early/2017/04/27/131680.full.pdf
* GNU Parallel is used in: Creates a speech dataset for deep learning https://github.com/jupiter126/Create_Speech_Dataset
* GNU Parallel is used in: Parse and process the demixing secrets dataset (DSD100) https://github.com/faroit/dsdtools
* First glance at the gnu parallel utility https://ibiscybernetics.com/blog/2017-04-05.html
* Installing parallel from source https://bitsanddragons.wordpress.com/2017/05/03/installing-parallel-from-source/
* How to run command or code in parallel in bash shell under Linux or Unix https://www.cyberciti.biz/faq/how-to-run-command-or-code-in-parallel-in-bash-shell-under-linux-or-unix/
* Parallel Serial Jobs Using GNU Parallel http://www.hpc.lsu.edu/training/weekly-materials/2017-Spring/gnuparallel-Feb2017.pdf
* GNU Parallel or How to list millions of S3 objects https://joeray.me/gnu-parallel-how-to-list-millions-objects.html
* Which Is the Best Tool for Copying a Large Directory Tree Locally? http://arjon.es/2017/05/11/which-is-the-best-tool-for-copying-a-large-directory-tree-locally/
<<Down https://springerplus.springeropen.com/articles/10.1186/s40064-016-2022-y>>
<<Wrong citation http://www.cell.com/cms/attachment/2095201602/2077415979/mmc1.pdf>>
<<Down http://www.nature.com/nprot/journal/v12/n5/full/nprot.2017.022.html?WT.feed_name=subjects_biotechnology>>
<<Citation not ok: https://arxiv.org/pdf/1704.08997.pdf>>
<<Probably http://www.sciencedirect.com/science/article/pii/S0044848616312194>>
<<Citation needed: https://sdstrowes.co.uk/publications/sdstrowes-rdns-aaaa.pdf>>
<<Citation not ok: https://www.nature.com/articles/s41598-017-01703-6>>
<<Probably http://www.sciencedirect.com/science/article/pii/S0044848616312194>>
<<Possibly http://link.springer.com/chapter/10.1007%2F978-3-319-22053-6_46>>
<<Possibly http://link.springer.com/article/10.1007/s12021-015-9290-5>>
<<Possibly http://link.springer.com/protocol/10.1007/978-1-4939-3578-9_14>>
<< kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>>
<<kontakt GNU Parallel was used (unfortunately without citation) in: Instrumentation and Trace Analysis for Ad-hoc Python Workflows in Cloud Environments http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=7214035>>
<<Har angiveligt submittet ny version - afventer opdatering>> GNU Parallel was used (unfortunately without citation) in: MUGBAS: a species free gene-based programme suite for post-GWAS analysis http://www.ncbi.nlm.nih.gov/pubmed/25765345

2
src/niceload
View file

@ -24,7 +24,7 @@
use strict;
use Getopt::Long;
$Global::progname="niceload";
$Global::version = 20170522;
$Global::version = 20170523;
Getopt::Long::Configure("bundling","require_order");
get_options_from_array(\@ARGV) || die_usage();
if($opt::version) {

2
src/parallel
View file

@ -1376,7 +1376,7 @@ sub check_invalid_option_combinations {
sub init_globals {
# Defaults:
$Global::version = 20170522;
$Global::version = 20170523;
$Global::progname = 'parallel';
$Global::infinity = 2**31;
$Global::debug = 0;

32
src/parallel.pod
View file

@ -341,7 +341,7 @@ B<:::> and B<::::> can be mixed. So these are equivalent:
::: 1 2 3
=item B<:::+> I<arguments> (alpha testing)
=item B<:::+> I<arguments> (beta testing)
Like B<:::> but linked like B<--link> to the previous input source.
@ -362,7 +362,7 @@ B<:::> and B<::::> can be mixed.
See B<-a>, B<:::> and B<--link>.
=item B<::::+> I<argfiles> (alpha testing)
=item B<::::+> I<argfiles> (beta testing)
Like B<::::> but linked like B<--link> to the previous input source.
@ -418,7 +418,7 @@ string that is not in the command line.
See also: B<:::>.
=item B<--bar> (alpha testing)
=item B<--bar> (beta testing)
Show progress as a progress bar. In the bar is shown: % of jobs
completed, estimated seconds left, and number of jobs started.
@ -656,7 +656,7 @@ variables, arrays, and functions) use B<env_parallel>.
See also: B<--record-env>.
=item B<--eta> (alpha testing)
=item B<--eta> (beta testing)
Show the estimated number of seconds before finishing. This forces GNU
B<parallel> to read all jobs before starting to find the number of
@ -744,9 +744,9 @@ See also: B<--line-buffer> B<--ungroup>
Print a summary of the options to GNU B<parallel> and exit.
=item B<--halt-on-error> I<val> (alpha testing)
=item B<--halt-on-error> I<val> (beta testing)
=item B<--halt> I<val> (alpha testing)
=item B<--halt> I<val> (beta testing)
When should GNU B<parallel> terminate? In some situations it makes no
sense to run all jobs. GNU B<parallel> should simply give up as soon
@ -891,7 +891,7 @@ specified, and for B<-I {}> otherwise. This option is deprecated;
use B<-I> instead.
=item B<--joblog> I<logfile> (alpha testing)
=item B<--joblog> I<logfile> (beta testing)
Logfile for executed jobs. Save a list of the executed jobs to
I<logfile> in the following TAB separated format: sequence number,
@ -1076,7 +1076,7 @@ Arguments will be recycled if one input source has more arguments than the other
See also B<--header>, B<:::+>, B<::::+>.
=item B<--load> I<max-load> (alpha testing)
=item B<--load> I<max-load> (beta testing)
Do not start new jobs on a given computer unless the number of running
processes on the computer is less than I<max-load>. I<max-load> uses
@ -1254,7 +1254,7 @@ control on the command line (used by GNU B<parallel> internally when
called with B<--sshlogin>).
=item B<--plus> (beta testing)
=item B<--plus>
Activate additional replacement strings: {+/} {+.} {+..} {+...} {..}
{...} {/..} {/...} {##}. The idea being that '{+foo}' matches the opposite of
@ -1767,7 +1767,7 @@ impossible to track which input block corresponds to which output.
B<--round-robin> implies B<--pipe>, except if B<--pipepart> is given.
=item B<--rpl> 'I<tag> I<perl expression>' (alpha testing)
=item B<--rpl> 'I<tag> I<perl expression>' (beta testing)
Use I<tag> as a replacement string for I<perl expression>. This makes
it possible to define your own replacement strings. GNU B<parallel>'s
@ -2236,7 +2236,7 @@ B<{}>.
B<--tagstring> is ignored when using B<-u>, B<--onall>, and B<--nonall>.
=item B<--tee> (beta testing)
=item B<--tee>
Pipe all data to all jobs. Used with B<--pipe>/B<--pipepart> and
B<:::>.
@ -2277,13 +2277,13 @@ different dir for the files. Setting B<--tmpdir> is equivalent to
setting $TMPDIR.
=item B<--tmux> (alpha testing)
=item B<--tmux> (beta testing)
Use B<tmux> for output. Start a B<tmux> session and run each job in a
window in that session. No other output will be produced.
=item B<--tmuxpane> (alpha testing)
=item B<--tmuxpane> (beta testing)
Use B<tmux> for output but put output into panes in the first window.
Useful if you want to monitor the progress of less than 100 concurrent
@ -2771,16 +2771,16 @@ foo) you can do:
If you want to remove a different ending, you can use {%string}:
parallel --plus echo {%_beta} ::: mycode_beta keep_beta_here
parallel --plus echo {%_demo} ::: mycode_demo keep_demo_here
You can also remove a starting string with {#string}
parallel --plus echo {#beta_} ::: beta_mycode keep_beta_here
parallel --plus echo {#demo_} ::: demo_mycode keep_demo_here
To remove a string anywhere you can use regular expressions with
{/regexp/replacement} and leave the replacement empty:
parallel --plus echo {/beta_/} ::: beta_mycode remove_beta_here
parallel --plus echo {/demo_/} ::: demo_mycode remove_demo_here
=head1 EXAMPLE: Download 24 images for each of the past 30 days

2
src/parset.pod
View file

@ -25,7 +25,7 @@ the destination variable and made to an array.
If I<variablename> contains multiple names separated by ',' or space,
the names will be the destination variables.
B<parset> is not production ready and alpha quality.
B<parset> is not production ready and is beta quality.
=head1 OPTIONS

2
src/sql
View file

@ -576,7 +576,7 @@ $Global::Initfile && unlink $Global::Initfile;
exit ($err);
sub parse_options {
$Global::version = 20170522;
$Global::version = 20170523;
$Global::progname = 'sql';
# This must be done first as this may exec myself