Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / bcgsc/longstitch issues and pull requests

#82 - IndexError: list index out of range

Issue - State: closed - Opened by mmpust 4 months ago - 5 comments

#81 - Unable to run LongStitch

Issue - State: closed - Opened by Oieswarya 6 months ago - 7 comments

#80 - Conda installation is non-functional

Issue - State: closed - Opened by drdna 8 months ago - 2 comments
Labels: Stale

#79 - Output files interpretation

Issue - State: closed - Opened by gforg34 9 months ago - 9 comments
Labels: question

#77 - import igraph as ig in ntlink_pair.py

Issue - State: closed - Opened by gforg34 9 months ago - 11 comments

#76 - Issues with module btllib in conda

Issue - State: closed - Opened by malvaradol 9 months ago - 8 comments

#75 - Input reads

Issue - State: closed - Opened by mikeqiu00 about 1 year ago - 4 comments
Labels: question, Stale

#74 - Fix path. Never hardcode a path, use long-to-linked-pe from PATH instead

Pull Request - State: closed - Opened by ccoulombe about 1 year ago - 3 comments

#74 - Fix path. Never hardcode a path, use long-to-linked-pe from PATH instead

Pull Request - State: closed - Opened by ccoulombe about 1 year ago - 3 comments

#73 - Prepare for release v1.0.5

Pull Request - State: closed - Opened by lcoombe over 1 year ago

#73 - Prepare for release v1.0.5

Pull Request - State: closed - Opened by lcoombe over 1 year ago

#72 - Document Tigmint's longmap parameter in help page, README

Pull Request - State: closed - Opened by lcoombe over 1 year ago

#72 - Document Tigmint's longmap parameter in help page, README

Pull Request - State: closed - Opened by lcoombe over 1 year ago

#71 - Support for HIFI data

Issue - State: closed - Opened by alexvasilikop over 1 year ago - 3 comments
Labels: enhancement, help wanted, question

#71 - Support for HIFI data

Issue - State: closed - Opened by alexvasilikop over 1 year ago - 3 comments
Labels: enhancement, help wanted, question

#70 - Socket.so: undefined symbol: Perl_xs_apiversion_bootcheck

Issue - State: closed - Opened by francicco over 1 year ago - 2 comments
Labels: Stale

#70 - Socket.so: undefined symbol: Perl_xs_apiversion_bootcheck

Issue - State: closed - Opened by francicco over 1 year ago - 2 comments
Labels: Stale

#69 - Input reads in format 'reads.fastq.gz' not found

Issue - State: closed - Opened by natforsdick over 1 year ago - 8 comments
Labels: bug

#69 - Input reads in format 'reads.fastq.gz' not found

Issue - State: closed - Opened by natforsdick over 1 year ago - 8 comments
Labels: bug

#68 - conda can't solve (dependencies?)

Issue - State: closed - Opened by mthon over 1 year ago - 5 comments

#68 - conda can't solve (dependencies?)

Issue - State: closed - Opened by mthon over 1 year ago - 5 comments

#67 - Estimating memory requirements for arks-long (core dump)

Issue - State: closed - Opened by Nicholas-Kron over 1 year ago - 9 comments

#67 - Estimating memory requirements for arks-long (core dump)

Issue - State: closed - Opened by Nicholas-Kron over 1 year ago - 9 comments

#65 - Finding Scaffold overlaps - Warning is empty

Issue - State: closed - Opened by benyoung93 over 1 year ago - 22 comments
Labels: Stale

#65 - Finding Scaffold overlaps - Warning is empty

Issue - State: closed - Opened by benyoung93 over 1 year ago - 22 comments
Labels: Stale

#64 - Longstitch with PacBio

Issue - State: closed - Opened by francicco over 1 year ago - 14 comments
Labels: question, Stale

#64 - Longstitch with PacBio

Issue - State: closed - Opened by francicco over 1 year ago - 14 comments
Labels: question, Stale

#63 - core dumped error in long-to-linked-pe step

Issue - State: closed - Opened by nirvana693 over 1 year ago - 6 comments
Labels: Stale

#63 - core dumped error in long-to-linked-pe step

Issue - State: closed - Opened by nirvana693 over 1 year ago - 6 comments
Labels: Stale

#62 - Hanging for >24h on "Finding pairs" step with no output

Issue - State: closed - Opened by pmcarlton almost 2 years ago - 8 comments

#62 - Hanging for >24h on "Finding pairs" step with no output

Issue - State: closed - Opened by pmcarlton almost 2 years ago - 8 comments

#61 - output filenames?

Issue - State: closed - Opened by margaretc-ho almost 2 years ago - 2 comments
Labels: question

#61 - output filenames?

Issue - State: closed - Opened by margaretc-ho almost 2 years ago - 2 comments
Labels: question

#60 - Longstitch "std::invalid_argument"

Issue - State: closed - Opened by MBinso almost 2 years ago - 3 comments
Labels: question

#60 - Longstitch "std::invalid_argument"

Issue - State: closed - Opened by MBinso almost 2 years ago - 3 comments
Labels: question

#59 - conda installation issues

Issue - State: closed - Opened by Laura-Alex almost 2 years ago - 3 comments
Labels: question

#59 - conda installation issues

Issue - State: closed - Opened by Laura-Alex almost 2 years ago - 3 comments
Labels: question

#58 - Prepare for release v1.0.4

Pull Request - State: closed - Opened by lcoombe almost 2 years ago

#58 - Prepare for release v1.0.4

Pull Request - State: closed - Opened by lcoombe almost 2 years ago

#57 - Update longstitch to allow uncompressed long reads input

Pull Request - State: closed - Opened by lcoombe almost 2 years ago

#57 - Update longstitch to allow uncompressed long reads input

Pull Request - State: closed - Opened by lcoombe almost 2 years ago

#56 - Allow LongStitch to accept uncompressed fasta and fastq files

Issue - State: closed - Opened by lcoombe almost 2 years ago - 1 comment
Labels: enhancement

#56 - Allow LongStitch to accept uncompressed fasta and fastq files

Issue - State: closed - Opened by lcoombe almost 2 years ago - 1 comment
Labels: enhancement

#55 - Longstitch stuck at "Running pairing stage of ntLink ..."

Issue - State: closed - Opened by Duda5 almost 2 years ago - 6 comments

#55 - Longstitch stuck at "Running pairing stage of ntLink ..."

Issue - State: closed - Opened by Duda5 almost 2 years ago - 6 comments

#54 - make: *** No rule to make target 'draft.fasta.fa', needed by 'draft.fasta.cut250.tigmint.fa'. Stop.`

Issue - State: closed - Opened by BenAawf almost 2 years ago - 3 comments
Labels: question

#54 - make: *** No rule to make target 'draft.fasta.fa', needed by 'draft.fasta.cut250.tigmint.fa'. Stop.`

Issue - State: closed - Opened by BenAawf almost 2 years ago - 3 comments
Labels: question

#53 - Problems with conda distribution of LongStitch

Issue - State: closed - Opened by BirdmanRidesAgain about 2 years ago - 11 comments

#53 - Problems with conda distribution of LongStitch

Issue - State: closed - Opened by BirdmanRidesAgain about 2 years ago - 11 comments

#52 - MAKE help text instead of Longstitch

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

#52 - MAKE help text instead of Longstitch

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

#51 - Prepare for release v1.0.3

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

#51 - Prepare for release v1.0.3

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

#50 - Add capability to use new ntLink features

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

#50 - Add capability to use new ntLink features

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

#49 - N sequences in scaffolded contig

Issue - State: closed - Opened by cytham over 2 years ago - 7 comments

#49 - N sequences in scaffolded contig

Issue - State: closed - Opened by cytham over 2 years ago - 7 comments

#48 - gunzip: standard input is a terminal -- ignoring

Issue - State: closed - Opened by giuliaguidi over 2 years ago - 6 comments

#48 - gunzip: standard input is a terminal -- ignoring

Issue - State: closed - Opened by giuliaguidi over 2 years ago - 6 comments

#47 - ntLink via brew failed

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

#47 - ntLink via brew failed

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

#46 - draft assembly

Issue - State: closed - Opened by antoine4ucsd over 2 years ago - 2 comments

#46 - draft assembly

Issue - State: closed - Opened by antoine4ucsd over 2 years ago - 2 comments

#45 - ImportError for pybedtools

Issue - State: closed - Opened by 123chenshixin over 2 years ago - 2 comments
Labels: Stale

#45 - ImportError for pybedtools

Issue - State: closed - Opened by 123chenshixin over 2 years ago - 2 comments
Labels: Stale

#44 - Problems with tigment when trying to run LongStitch

Issue - State: closed - Opened by Lean-s over 2 years ago - 7 comments

#44 - Problems with tigment when trying to run LongStitch

Issue - State: closed - Opened by Lean-s over 2 years ago - 7 comments

#43 - Sort order on bed file

Issue - State: closed - Opened by skitchen19 over 2 years ago - 6 comments
Labels: Stale

#43 - Sort order on bed file

Issue - State: closed - Opened by skitchen19 over 2 years ago - 6 comments
Labels: Stale

#42 - Prepare for release v1.0.2

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

#42 - Prepare for release v1.0.2

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

#41 - Add options for output scaffolds file prefix, making required soft links

Pull Request - State: closed - Opened by lcoombe over 2 years ago - 3 comments
Labels: enhancement

#41 - Add options for output scaffolds file prefix, making required soft links

Pull Request - State: closed - Opened by lcoombe over 2 years ago - 3 comments
Labels: enhancement

#40 - Add snakemake wrapper

Issue - State: open - Opened by KristinaGagalova over 2 years ago - 5 comments
Labels: enhancement

#40 - Add snakemake wrapper

Issue - State: open - Opened by KristinaGagalova over 2 years ago - 5 comments
Labels: enhancement

#39 - Longstitch Freezing/"No rule to make target"

Issue - State: closed - Opened by jwalewski almost 3 years ago - 26 comments

#39 - Longstitch Freezing/"No rule to make target"

Issue - State: closed - Opened by jwalewski almost 3 years ago - 26 comments

#38 - Fix parameter 'a' collision between ntLink and ARKS-long

Pull Request - State: closed - Opened by lcoombe almost 3 years ago
Labels: bug

#38 - Fix parameter 'a' collision between ntLink and ARKS-long

Pull Request - State: closed - Opened by lcoombe almost 3 years ago
Labels: bug

#37 - Specifying -a parameter for ARCS through LongStitch

Issue - State: closed - Opened by aakashsur almost 3 years ago - 2 comments
Labels: bug

#37 - Specifying -a parameter for ARCS through LongStitch

Issue - State: closed - Opened by aakashsur almost 3 years ago - 2 comments
Labels: bug

#36 - Broken Pipe Error

Issue - State: closed - Opened by ChemaMD almost 3 years ago - 2 comments
Labels: question, Stale

#36 - Broken Pipe Error

Issue - State: closed - Opened by ChemaMD almost 3 years ago - 2 comments
Labels: question, Stale

#29 - tigmint_molecule MolecIdentifier module fails to be imported

Issue - State: closed - Opened by camilogarciabotero almost 3 years ago - 6 comments
Labels: Stale

#29 - tigmint_molecule MolecIdentifier module fails to be imported

Issue - State: closed - Opened by camilogarciabotero almost 3 years ago - 6 comments
Labels: Stale

#28 - CI Fixes

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

#28 - CI Fixes

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

#27 - adjusting minimap2 arguments to accommodate different types of long reads

Issue - State: closed - Opened by bishopia almost 3 years ago - 2 comments
Labels: documentation, question

#27 - adjusting minimap2 arguments to accommodate different types of long reads

Issue - State: closed - Opened by bishopia almost 3 years ago - 2 comments
Labels: documentation, question

#26 - quick crash due to make errors for default run.

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

#26 - quick crash due to make errors for default run.

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

#25 - Pipeline without Tigmint doesn't run

Issue - State: closed - Opened by charlesfeigin about 3 years ago - 3 comments
Labels: question

#25 - Pipeline without Tigmint doesn't run

Issue - State: closed - Opened by charlesfeigin about 3 years ago - 3 comments
Labels: question

#24 - make error

Issue - State: closed - Opened by seanschoville about 3 years ago - 5 comments
Labels: question

#24 - make error

Issue - State: closed - Opened by seanschoville about 3 years ago - 5 comments
Labels: question

#23 - $draft.cut$cut.tigmint.fa is empty

Issue - State: closed - Opened by rwhetten about 3 years ago - 18 comments

#23 - $draft.cut$cut.tigmint.fa is empty

Issue - State: closed - Opened by rwhetten about 3 years ago - 18 comments