pachterlab/ffq issues and pull requests

#74 - Extract parser from main command.

Pull Request - State: open - Opened by njohner 6 months ago

#73 - sample search gets NoneType' object has no attribute 'text'

Issue - State: closed - Opened by diekhans 6 months ago - 2 comments
Labels: Stale

#72 - add CRX accession parsing

Issue - State: closed - Opened by sbooeshaghi 7 months ago - 2 comments
Labels: Stale

#71 - access original uploaded bam files from SRA?

Issue - State: closed - Opened by whtns 9 months ago - 1 comment
Labels: Stale

#70 - ERROR 'str' object has no attribute 'copy'

Issue - State: closed - Opened by holmrenser 9 months ago - 2 comments
Labels: Stale

#69 - ffq --ftp file not found

Issue - State: closed - Opened by hariesramdhani 11 months ago - 2 comments

#68 - How to Download Files Requiring a Key with prefetch

Issue - State: closed - Opened by Lin-zikai 11 months ago - 1 comment
Labels: Stale

#67 - ffq not working anymore (ffq: error)

Issue - State: closed - Opened by rderelle 11 months ago - 2 comments

#66 - Fix: Remove trailing slash from ENA URL in get_xml

Pull Request - State: closed - Opened by hazirliver 11 months ago - 1 comment

#65 - No sample found for any GEO entries

Issue - State: closed - Opened by NaotoKubota 11 months ago - 5 comments

#64 - ffq

Issue - State: closed - Opened by BaHole 11 months ago - 3 comments

#63 - id stored in variable

Issue - State: closed - Opened by rominaappierdo over 1 year ago

#62 - ffq [DOI]

Issue - State: closed - Opened by kylekimler over 1 year ago - 3 comments
Labels: Stale

#61 - Question on ffq [DOIS]

Issue - State: closed - Opened by ScienceComputing over 1 year ago - 2 comments

#60 - Work around failures in ENA XML retrieval to still produce useful info

Pull Request - State: open - Opened by pinin4fjords over 1 year ago

#59 - [enhancement] Generate Aspera URL

Issue - State: closed - Opened by davetang almost 2 years ago - 1 comment
Labels: Stale

#58 - Private GSEs

Issue - State: closed - Opened by lakigigar almost 2 years ago - 1 comment
Labels: Stale

#57 - Error: ffq GSE10320

Issue - State: closed - Opened by srp33 almost 2 years ago - 2 comments
Labels: Stale

#56 - Couldn't find a tree builder with the features you requested: xml. Do you need to install a parser library?

Issue - State: closed - Opened by aaditkapoor almost 2 years ago - 1 comment
Labels: Stale

#55 - Bump wheel from 0.34.2 to 0.38.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#54 - How open are you to larger contributions?

Issue - State: closed - Opened by Midnighter about 2 years ago - 3 comments
Labels: Stale

#53 - Convert json output to a tsv

Issue - State: closed - Opened by apredeus about 2 years ago - 1 comment
Labels: Stale

#52 - nextflow pipeline using ffq to download reads

Pull Request - State: closed - Opened by telatin over 2 years ago - 3 comments

#51 - feature request: return metadata when no fastq available

Issue - State: closed - Opened by crazyhottommy over 2 years ago - 1 comment

#50 - Fetching metadata from NCBI

Issue - State: closed - Opened by Sorcery229 over 2 years ago - 1 comment

#49 - Conda version out of date

Issue - State: closed - Opened by half-adder over 2 years ago - 3 comments

#48 - biosample error

Issue - State: closed - Opened by PAMorin over 2 years ago - 3 comments
Labels: Stale

#47 - Prepping for release

Pull Request - State: closed - Opened by sbooeshaghi over 2 years ago

#46 - Fix --split

Pull Request - State: closed - Opened by telatin over 2 years ago - 3 comments

#45 - Add —version flag

Pull Request - State: closed - Opened by andersgs over 2 years ago - 1 comment

#44 - Add version string

Pull Request - State: closed - Opened by andersgs over 2 years ago - 3 comments

#43 - Add --version flag

Issue - State: closed - Opened by andersgs over 2 years ago - 1 comment

#42 - No AWS links parsed (for run SRR8387856)

Issue - State: closed - Opened by konsolerr over 2 years ago - 2 comments

#41 - ERROR Couldn't find a tree builder with the features you requested: xml.

Issue - State: closed - Opened by chaimol over 2 years ago - 2 comments

#40 - ERROR object of type 'NoneType' has no len()

Issue - State: closed - Opened by FFinotello over 2 years ago - 4 comments

#39 - Fix --split

Pull Request - State: closed - Opened by telatin over 2 years ago - 7 comments

#38 - `--split` throws an error

Issue - State: closed - Opened by telatin over 2 years ago - 1 comment

#37 - suggestion: add --api-key KEY

Issue - State: closed - Opened by telatin over 2 years ago - 1 comment
Labels: enhancement, Stale

#36 - New pull request for nose -> pytest against devel

Pull Request - State: closed - Opened by lauraluebbert over 2 years ago - 1 comment

#35 - nose -> pytest; adjustments for Python 3.9 and 3.10

Pull Request - State: closed - Opened by lauraluebbert over 2 years ago - 1 comment

#34 - PRJNA format Bioproject support

Issue - State: closed - Opened by Nusob888 over 2 years ago - 5 comments
Labels: enhancement, Stale

#33 - [Feature] project level support

Issue - State: closed - Opened by alienzj over 2 years ago - 2 comments

#32 - aws example no longer works

Issue - State: closed - Opened by gordonaa over 2 years ago - 4 comments

#31 - Refactor for running as a library.

Pull Request - State: closed - Opened by ewels over 2 years ago - 2 comments

#30 - Tests framework `nose` no longer maintained

Issue - State: closed - Opened by ewels over 2 years ago - 2 comments

#29 - Import refactoring

Pull Request - State: closed - Opened by ewels over 2 years ago - 3 comments

#28 - HTTPError' object has no attribute 'getcode' and HTTP 401

Issue - State: closed - Opened by FrankMaiwald over 2 years ago - 1 comment

#27 - Network unreachable behind proxy

Issue - State: closed - Opened by karl-az over 2 years ago - 8 comments
Labels: enhancement, Stale

#26 - HTTP 404 Error

Issue - State: closed - Opened by mfansler over 2 years ago - 2 comments

#25 - ERROR 429 Client Error: Too Many Requests for url

Issue - State: closed - Opened by mfansler over 2 years ago - 1 comment

#24 - Incomplete metadata obtained

Issue - State: closed - Opened by Chengwei94 over 2 years ago - 1 comment

#23 - False metadata fetched when using BioSample accession number

Issue - State: closed - Opened by trickovicmatija over 2 years ago - 8 comments

#22 - fetchngs + ffq = <3 ?

Issue - State: closed - Opened by Midnighter over 2 years ago - 2 comments

#21 - Enhancements

Issue - State: closed - Opened by sbooeshaghi over 2 years ago - 2 comments
Labels: enhancement, Stale

#20 - Improve tests

Issue - State: closed - Opened by sbooeshaghi over 2 years ago - 1 comment
Labels: enhancement, Stale

#19 - Connection reset

Issue - State: closed - Opened by Jigyasa3 almost 3 years ago - 2 comments

#18 - prepping for ffq release

Pull Request - State: closed - Opened by agalvezm almost 3 years ago

#17 - new ffq release

Pull Request - State: closed - Opened by agalvezm almost 3 years ago

#16 - `ffq` does not work for some low-number SRRs

Issue - State: closed - Opened by jbloom over 3 years ago - 2 comments

#15 - merge devel into master

Pull Request - State: closed - Opened by Lioscro over 3 years ago

#14 - merge devel into master

Pull Request - State: closed - Opened by Lioscro over 3 years ago

#13 - requirements.txt in pypi source file

Issue - State: closed - Opened by druvus over 3 years ago

#12 - conda installation

Issue - State: closed - Opened by mweberr over 3 years ago - 7 comments

#11 - ERROR 'NoneType' object has no attribute 'text'

Issue - State: closed - Opened by lakigigar over 3 years ago - 2 comments

#10 - Bug fixes and improvements

Pull Request - State: closed - Opened by sbooeshaghi over 3 years ago

#9 - Incomplete output from DOI

Issue - State: closed - Opened by GeoMicroSoares over 3 years ago - 3 comments

#8 - unable to retrieve non-SRR runs (DRR and ERR runs)

Issue - State: closed - Opened by kaylajohnson over 3 years ago - 5 comments

#7 - less verbose logging

Pull Request - State: closed - Opened by Lioscro over 4 years ago

#6 - Merge devel into master

Pull Request - State: closed - Opened by Lioscro over 4 years ago

#5 - ffq crashes when run has no data

Issue - State: closed - Opened by sbooeshaghi over 4 years ago - 3 comments
Labels: bug

#4 - Merge devel into master

Pull Request - State: closed - Opened by Lioscro over 4 years ago

#3 - Added unit tests, added abstract and title to study for GSE

Pull Request - State: closed - Opened by sbooeshaghi over 4 years ago

#2 - SRP, DOI, TITLE

Pull Request - State: closed - Opened by Lioscro over 4 years ago

#1 - Enable variable length SRRs

Issue - State: closed - Opened by sbooeshaghi over 4 years ago - 2 comments
Labels: bug, enhancement

GitHub / pachterlab/ffq issues and pull requests