- Apr 01, 2020
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Ian Fiddes authored
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Ian Fiddes authored
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- Mar 31, 2020
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Ian Fiddes authored
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Ian Fiddes authored
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Ian Fiddes authored
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Ian Fiddes authored
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Ian Fiddes authored
1. Test conda env in addition to docker env. 2. Remove unnecessary dependencies.
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- Feb 23, 2020
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Ian Fiddes authored
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- Dec 11, 2019
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Ian Fiddes authored
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Ian Fiddes authored
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- Dec 09, 2019
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Ian Fiddes authored
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- Dec 01, 2019
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Ian Fiddes authored
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- Nov 07, 2019
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Ian Fiddes authored
Re-write the pairwise alignment step to use the parasail alignment library instead of BLAT.
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- Nov 04, 2019
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Ian Fiddes authored
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Ian Fiddes authored
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- Jan 09, 2019
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Joel Armstrong authored
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- Nov 01, 2018
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Ian Fiddes authored
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- Oct 23, 2018
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Alana Alexander authored
Removed "bedtools" from the necessary kent utilities list (because it is installed as a standalone)
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- Sep 05, 2018
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Ian Fiddes authored
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- Aug 24, 2018
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Chang Kim authored
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- Aug 20, 2018
- Aug 01, 2018
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Joel Armstrong authored
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- Jun 29, 2018
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Joel Armstrong authored
wigToBigWig is needed by part of the pipeline, and bd2k-python-lib seems to be needed. It was previously installed when installing toil, but later versions of toil don't need it anymore.
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- Mar 06, 2018
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Ian Fiddes authored
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- Mar 05, 2018
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Ian Fiddes authored
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- Dec 19, 2017
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Ian Fiddes authored
For issue #76.
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- Dec 04, 2017
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Ian Fiddes authored
1. Store metrics, added a plot. 2. Perform a gene overlap analysis step at the end of consensus finding to ensure no novel predictions lead to problems. 3. Fixed some bugs in the old implementation. 4. Updated documentation to reflect these changes.
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- Oct 05, 2017
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Ian Fiddes authored
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Ian Fiddes authored
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- Oct 04, 2017
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Ian Fiddes authored
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- Aug 25, 2017
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Ian Fiddes authored
I mistakenly went back to transMapPostChain, when mark had re-named it pslMapPostChain for the Kent repo. Make the augustus improvement plots not have huge file sizes by rasterizing the plot. Updates to documentation. Related to issues #62 and #63.
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- Aug 22, 2017
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Ian Fiddes authored
Not all augustus species have UTR models. In this case, the user needs to be able to turn this flag off.
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- Aug 21, 2017
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Ian Fiddes authored
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- Aug 16, 2017
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Ian Fiddes authored
GFF3 parsing no longer relies on the slow GFF3 library, and instead relies on using the `-attrsOut` flag from `gff3ToGenePred` to construct features. A best attempt is made to parse GENCODE, Ensembl and NCBI format GFF3. Bring on the new edge cases!
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- Jul 31, 2017
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Ian Fiddes authored
Protein FASTA files can now be introduced via the [PROTEIN_FASTA] section in the config file. Based on the genomes listed in the file, these will be aligned and used for AugustusTM(R) and AugustusCGP. This should greatly help with CGP predictions in more distantly related species. TODO: 1. Talk to Mario and Stefanie about adjusting the CDS/CDSpart bonus/malus in the config files. 2. Allow for arbitrary pre-generated hints files to also be included.
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- Jul 07, 2017
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Ian Fiddes authored
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- May 31, 2017
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Ian Fiddes authored
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- Mar 28, 2017
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Ian Fiddes authored
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- Mar 21, 2017
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Ian Fiddes authored
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