Difference between revisions of "Deprecation"
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| Line 51: | Line 51: | ||
* most - 20160721 | * most - 20160721 | ||
* rnaquast - 1.2.0 | * rnaquast - 1.2.0 | ||
| − | * | + | * sdt - 1.2 |
| + | * marygold - 0.2 | ||
| + | * kmergenie - 1.6741 | ||
| + | * haptree - 1.0 | ||
| + | * hmmsplicer - 0.9.5 | ||
| + | * mocat - 1.3r2, 2.0 | ||
| + | * metamos - 1.5.0rc4-20140827 | ||
| + | * iclipro - 0.1.1 | ||
| + | * bamreadcount - 20150216 | ||
| + | * spark - 2.1.0 | ||
| + | * falcon_unzip - 20160623 | ||
| + | * pbcommand - 20151203 | ||
| + | * stacks 1.05, 1.18, 1.21, 1.24, 1.35, 1.45, 1.48 | ||
| + | * poretools - 0.5.0 | ||
| + | * transabyss - 1.5.4 | ||
| + | * orthofinder - 0.2.5, 0.6.0, 2.1.2, 2.2.1, 2.2.3, 2.2.6, 2.2.7, 2.3.3, 2.3.8 | ||
| + | * snappy - 1.2.1 | ||
| + | * reago - 1.1 | ||
| + | * srst2 - 0.2.0 | ||
| + | * spades - 3.0.0, 3.1.0, 3.5.0, 3.6.0, 3.6.2, 3.9.0, 3.10.0 | ||
;2020-04-01: | ;2020-04-01: | ||
Revision as of 22:30, 23 April 2020
Apps and Databases to Remove
A list of software and the databases that are going to be deprecated. The modules are removed and the software is put into the REMOVE directories to be removed 6 months from being added to this page.
Core Applications
- 2020-05-01
- opencv - 2.4.8 - gcc/4.7.2
- rnaskim - .20140625 - gcc/4.7.2
- syzygy - 1.2.7 - gcc/4.7.2
- cgat - 0.2.3
- pyrad - 3.0.63
- ddocent - 20160425
- ceas - 1.0.2
- metassembler - 1.5
- dapars - 0.9.0
- miso - 0.5.2
- anvio - 2.0.0
- phyluce - 20140427, 20151103, 20160715
- conifer - 0.2.2
- bsmap - 2.74
- seqmagick - 20150923
- clipper 1.0
- fast-iclip - 0.9.1
- bedops - 2.4.2
- mats - 2.1.0, 3.2.1.beta
- arc - 20140305, 20140312
- cellprofiler - 2.0, 2.2.0
- peer - 20120508
- busco - 2.0b
- agalm - 0.3.5
- pbsmrtpipe - 20151202
- afni - 2016_0_19-openmpi, 2016_2_09
- gsutil - 4.15
- agalma - 0.5.0
- meme - 4.8.1
- binsanity - 0.1.3, 0.2.5.9
- exomcnv - 1.4
- last - 193, 247, 531
- sweep - 20160211
- shannon - 20160211
- shorah - 20130830, 20131204
- treecorr - 3.2.3
- ngscat - 0.1
- cufflinks - 2.2.0
- ectools - 20140311, 20141201
- concoct - 0.3.1
- bcbio-nextgen - 0.8.7
- ale - 20150507
- cerulean - 0.1
- most - 20160721
- rnaquast - 1.2.0
- sdt - 1.2
- marygold - 0.2
- kmergenie - 1.6741
- haptree - 1.0
- hmmsplicer - 0.9.5
- mocat - 1.3r2, 2.0
- metamos - 1.5.0rc4-20140827
- iclipro - 0.1.1
- bamreadcount - 20150216
- spark - 2.1.0
- falcon_unzip - 20160623
- pbcommand - 20151203
- stacks 1.05, 1.18, 1.21, 1.24, 1.35, 1.45, 1.48
- poretools - 0.5.0
- transabyss - 1.5.4
- orthofinder - 0.2.5, 0.6.0, 2.1.2, 2.2.1, 2.2.3, 2.2.6, 2.2.7, 2.3.3, 2.3.8
- snappy - 1.2.1
- reago - 1.1
- srst2 - 0.2.0
- spades - 3.0.0, 3.1.0, 3.5.0, 3.6.0, 3.6.2, 3.9.0, 3.10.0
- 2020-04-01
- tophat - 2.0.8b, 2.0.1, 2.0.13, 2.0.11, 1.4.1, 1.3.3b, 1.3.0
- MATS - 3.0.4.beta, 3.0.6.beta, 3.0.8
- afni - 2011_12_21_1014, 2013_05_31, 2013_11_24-openmp
- agalma - 0.2.1
- amuse - 6.0
- arc - 20130715
- bayesrate - 1.3.43
- beta - 1.0.5
- cgat - 0.2.3
- cufflinks - 1.3.0, 2.0.0, 2.0.2
- emirge - 20130727
- eval - 2.2.8
- htseq - 0.5.3p3, 0.6.1p1
- libsvm - 3.12
- lsc - 0.3.1, 0.3, 1alpha, 1beta, 2.0
- maker - 2.10, 2.25b
- metamos - 1.3.1
- miso - 0.4.4, 0.4.9
- modeller - 9.11, 9.13
- msmbuilder - 2.5.1
- nexuscl - 2.1.18
- ngsutils - 20130722, 20150206
- partitionfinder - 1.0.1, 2.0.0-pre8, 2.0.0-pre10, 2.0.0-pre11
- phycas - 1.2.0
- scons - 2.3.0
- spades - 2.5.0, 2.5.1 - More will be removed in the future some are loaded as dependencies
- spanki - 0.4.1, 0.4.3, 0.5.0
- sparcc - 201402
- spimap - 1.1, .1.1.git20120501
- treefix - 1.1.10, 1.1.7
- vcflib - 20121207, 20141119
- velvet - 1.2.06, 1.2.07
- wgs - 7.0.1.23-pacbio, 7.0.1.23, 8.0.r4443-pacbio, 8.0.r4443
- idba-ud - 1.0.9, 1.1.0
- freebayes - 0.9.13, 0.9.14, 0.9.6, 0.9.7, 0.9.9.2
- 2020-03-26
- python/2.6.8
- python/2.7.3
- 2020-03-01
- homer - 20130529, 4.5, 4.6, 4.7, databases
- fgenesb - 2012, databases
- picrust - 1.0.0-gx
- qiime - 1.5.0, 1.6.0, 1.8.0, 1.9.0
- iprscan - 4.8, 5.0rc6, 5.19-58.0, 5.24-63.0, 5.25-64.0, 5.26-65.0, 5.29-68.0.bak, database
CUDA 9 Applications
- 2020-04-01
- Guppy - 2.3.5, 2.3.7, 3.1.5, 3.2.1, 3.2.2
- beagle - 3.0.2.20181009, 3.0.1.20180607