Skip to main content
This is a pre-production deployment of Warehouse. Changes made here affect the production instance of PyPI (pypi.python.org).
Help us improve Python packaging - Donate today!
Avatar for jeremiahsavage from gravatar.com

jeremiahsavage

  Joined on Dec 14, 2015

41 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 Jul 3, 2017

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

bunny_runtime_metrics_sqlite

Last released on Sep 21, 2017

store bunny runtime metrics in sqlite

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

dnaseq_queue_status

Last released on May 31, 2017

write db status

dnaseq_validation

Last released on May 9, 2017

validate dnaseq workflow based on fastqc, picard and samtools metrics

fastqc_db

Last released on Oct 25, 2017

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

fastqvalidator_sqlite

Last released on Jul 19, 2017

store fastqvalidator metrics in sqlite

integrity_to_sqlite

Last released on Oct 26, 2017

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

json-to-sqlite

Last released on Oct 25, 2017

convert to json to column based sqlite

merge_sqlite

Last released on Oct 26, 2017

merge arbitrary number of sqlite files

optityper_to_sqlite

Last released on Feb 4, 2017

store optityper metrics in sqlite

picard_metrics_sqlite

Last released on Oct 25, 2017

store picard metrics in sqlite

picard_tool

Last released on Jul 26, 2016

call picard tools and store time/mem metrics in sqlitedb

queue_bqsr_status

Last released on Mar 29, 2017

write bqsr db status

queue_coclean_status

Last released on Jan 30, 2017

write coclean db status

queue_hlatype_status

Last released on Feb 3, 2017

write hlatyping db status

queue_status

Last released on Sep 29, 2016

write db status

readgroup_json_db

Last released on Oct 25, 2017

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 Oct 26, 2017

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 Oct 25, 2017

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

star_metrics_sqlite

Last released on Jul 20, 2017

store star metrics in sqlite

table_string_sqlite_cell

Last released on Mar 27, 2017

create a single cell table with a value

Supported By

WebFaction WebFaction Technical Writing Elastic Elastic Search Pingdom Pingdom Monitoring Dyn Dyn DNS Sentry Sentry Error Logging CloudAMQP CloudAMQP RabbitMQ Heroku Heroku PaaS Kabu Creative Kabu Creative UX & Design Fastly Fastly CDN DigiCert DigiCert EV Certificate Rackspace Rackspace Cloud Servers DreamHost DreamHost Log Hosting