This is a pre-production deployment of Warehouse, however changes made here WILL affect the production instance of PyPI.
jeremiahsavage

jeremiahsavage

Joined on Dec 14, 2015

Projects

bam_add_eof

Last released on Jun 24, 2016

if a BAM is missing EOF, add it, else output original BAM

bam_readgroup_to_json

Last released on Oct 26, 2016

convert each readgroup id to a json file from a BAM

bam_reheader

Last released on Aug 26, 2016

reheader a BAM to include GDC @SQ info

bamutil_tool

Last released on Dec 17, 2015

call bamutil tools and store time/mem metrics in sqlitedb

biobambam_tool

Last released on Jun 15, 2016

call biobambam tools and store time/mem metrics in sqlitedb

bwa_pe_tool

Last released on Jul 11, 2016

map PE fastq reads to a reference genome with bwa

bwa_se_tool

Last released on Jun 29, 2016

map SE fastq reads to a reference genome with bwa

bwa_tool

Last released on Jun 30, 2016

map PE fastq reads to a reference genome with bwa

cdis_pipe_utils

Last released on Jun 13, 2016

Reusable code to call pipeline tools and get time/mem metrics

cgquery_xml_to_bamlibrary_capture_json

Last released on Sep 21, 2016

convert cgquery sra xml to capture_kits/target_set json

decider_bwa_pe

Last released on Jul 11, 2016

match readgroup and fastq outputs

decider_bwa_se

Last released on Jul 11, 2016

match readgroup and fastq outputs

fastqc_db

Last released on Aug 11, 2016

store FastQC data/summary in sqlitedb

fastqc_sqlite

Last released on Apr 19, 2016

store FastQC data/summary in sqlitedb

fastqc_to_json

Last released on Nov 15, 2016

fastqc to json for bwa cwl

fastqc_tool

Last released on Jun 15, 2016

call fastqc tools and store time/mem metrics in sqlitedb

fastq_remove_duplicate_qname

Last released on Aug 31, 2016

remove duplicate QNAME from a fastq

integrity_to_sqlite

Last released on Aug 31, 2016

store `ls -l`, `md5sum` and `sha256sum` to sqlite

merge_sqlite

Last released on Aug 4, 2016

merge arbitrary number of sqlite files

picard_metrics_sqlite

Last released on Sep 11, 2016

store picard metrics in sqlite

picard_tool

Last released on Jul 26, 2016

call picard tools and store time/mem metrics in sqlitedb

queue_status

Last released on Sep 29, 2016

write db status

readgroup_json_db

Last released on Aug 22, 2016

read readgroup data as json and store in sqlitedb

readgroup_platform_insertion

Last released on Mar 23, 2016

Insert a PL:<value> in @RGs in a BAM header

remove_duplicate_fastq_matepair

Last released on Jun 24, 2016

Remove duplicate mate pairs from a FASTQ

remove_qcfailed_mapped

Last released on Jan 4, 2016

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

samtools_metrics_sqlite

Last released on Jul 25, 2016

store samtools metrics in sqlite

samtools_tool

Last released on Jun 15, 2016

call samtools tools and store time/mem metrics in sqlitedb

sqlite_to_postgres

Last released on Aug 9, 2016

write sqlite file to postgres

sra_hs_lookup

Last released on Jan 4, 2016

call remove_qcfailed_mapped and store time/mem metrics in sqlitedb

Supported By

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