dsprint-pipeline's People
dsprint-pipeline's Issues
PertInInt relies on filenames to determine domain names
Line 173 in 6e97c09
This is a hack which only works for the ig
domain. Need to investigate pertInInt code and decouple it from filenames, and/or generate the correctly named files before calling pertInInt.
Biopython version
Bio.Alphabet
has been removed from biopython>=1.78 as per:
https://biopython.org/wiki/Alphabet
Till dsprint-pipeline is tweaked to work with the latest biopython versions, biopython will be pinned to version 1.77 in `environment.yml'
Ambiguous rule with latest snakemake
With snakemake version 5.27.4, we're getting the following error on running the step for downloading data:
snakemake --cores 1 --use-conda --until download_exac download_exac_coverage download_hg19_2bit download_uniprot_fasta download_uniprot_idmapping download_phastCons download_phyloP download_pertinint_mafs install_pertinint install_hmmer2 install_hmmer3 install_tabix install_twoBitToFa --dryrun
AmbiguousRuleException:
Rules pertinint_compute_jsd and pertinint_verify_exons are ambiguous for the file /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt.
Consider starting rule output with a unique prefix, constrain your wildcards, or use the ruleorder directive.
Wildcards:
pertinint_compute_jsd: chromosome=1
pertinint_verify_exons: chromosome=1.jsd.txt
Expected input files:
pertinint_compute_jsd: pertinint-internal/config.py /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1 /scratch/gpfs/vineetb/dsprint2/pertinint/ucscgb/hg19alignment/mafs/chr1.maf.gz
pertinint_verify_exons: pertinint-internal/config.py /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/Homo_sapiens.GRCh37.pep.all.withgenelocs.fa.gz /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/dna_smExpected output files:
pertinint_compute_jsd: /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt
pertinint_verify_exons: /scratch/gpfs/vineetb/dsprint2/pertinint/ensembl/Homo_sapiens.GRCh37/exons/1.jsd.txt
Till this is resolved, snakemake will be pinned to version 5.19.2 in requirements.txt
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. ๐๐๐
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google โค๏ธ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.