Ecosyste.ms: Issues

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

GitHub / blahah/transrate issues and pull requests

#254 - Transrate conda

Pull Request - State: closed - Opened by pmomadeira 4 months ago - 1 comment

#253 - Linux binary for v1.0.3 cannot be downloaded

Issue - State: open - Opened by fran-romero-campero 10 months ago - 2 comments

#252 - Update snap.rb to fix failure to build index

Pull Request - State: open - Opened by IdoBar 11 months ago

#251 - Transrate FASTQ based run not working

Issue - State: open - Opened by Gruxxis about 1 year ago - 1 comment

#250 - Compiled repo link is obsolete

Issue - State: open - Opened by asan-emirsaleh almost 2 years ago

#249 - salmon version to be installed by --install-deps=all

Issue - State: open - Opened by asan-emirsaleh almost 2 years ago

#248 - Snap index error

Issue - State: open - Opened by asan-emirsaleh almost 2 years ago - 4 comments

#247 - salmon: error while loading shared libraries

Issue - State: open - Opened by Liyong-Zhang about 2 years ago - 1 comment

#246 - merge assemblies

Issue - State: open - Opened by ewelinarubin over 2 years ago - 1 comment

#245 - Linux download not working v1.0.3

Issue - State: open - Opened by Tina-L-Nguyen about 3 years ago - 1 comment

#244 - Conda installation fails based on 'glibc' dependency issue

Issue - State: closed - Opened by timslittle over 3 years ago - 1 comment

#243 - supported bridges.csv missing from output

Issue - State: open - Opened by Shabbirm21 over 3 years ago

#242 - Broken link to obtain code

Issue - State: open - Opened by chrisreidy almost 4 years ago - 1 comment

#241 - weird results (v1.0.3)

Issue - State: open - Opened by manuelsmendoza over 4 years ago - 5 comments

#240 - Failed to install-deps

Issue - State: open - Opened by Gyzele over 4 years ago - 21 comments

#239 - Discrepancy in ORF count between contigs.csv and assemblies.csv

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

#238 - transrate with 2left and 2 right fastq files?

Issue - State: closed - Opened by VaneSGT over 4 years ago - 3 comments

#236 - Depend on salmon 0.7.2

Pull Request - State: open - Opened by gbrsales about 5 years ago

#235 - SNAP error in Transrate with large dataset

Issue - State: open - Opened by upendra2020 about 5 years ago - 1 comment

#234 - Not able to install transrate (ruby error) ?

Issue - State: open - Opened by sunnyEV about 5 years ago

#232 - SNAP error

Issue - State: open - Opened by zolotarovgl over 5 years ago - 1 comment

#231 - MPI implementation

Issue - State: open - Opened by rafaeltiveron over 5 years ago - 1 comment

#230 - Transrate broken and unsupported?

Issue - State: closed - Opened by Shellfishgene over 5 years ago - 4 comments

#229 - tpm, eff_count, and coverage all zero in contigs.csv

Issue - State: open - Opened by matthewabirk almost 6 years ago - 1 comment

#228 - Snap found unmatched read IDs in input fastq files

Issue - State: open - Opened by elainfl almost 6 years ago - 2 comments

#227 - The solvation of librt.so.1 in Ubuntu 16.04 server

Issue - State: open - Opened by life404 almost 6 years ago - 2 comments

#226 - transrate in conda project

Issue - State: closed - Opened by manuelsmendoza about 6 years ago - 4 comments

#225 - Snap failing due to memory requirements on large transcriptomes

Issue - State: open - Opened by kvpmulder about 6 years ago - 2 comments

#224 - Salmon is failing

Issue - State: open - Opened by sagnikbanerjee15 over 6 years ago - 4 comments

#223 - Salmon

Issue - State: open - Opened by OnlyHigh over 6 years ago - 1 comment

#222 - Using current version of Salmon

Issue - State: open - Opened by algebio over 6 years ago

#221 - CPU instruction shared across concurrent transrate runs

Issue - State: open - Opened by Jeremias-Brand almost 7 years ago

#220 - Unexpectedly low `p fragments mapped`

Issue - State: open - Opened by kmnip almost 7 years ago

#219 - Dependencies are missing -salmon (0.6.0)

Issue - State: open - Opened by Portvin almost 7 years ago - 1 comment

#218 - SNAP failing in v 1.0.3

Issue - State: open - Opened by ssander5 almost 7 years ago - 5 comments

#217 - Weird read mapping metrics on version 1.0.3

Issue - State: open - Opened by RuiMMFaria about 7 years ago

#216 - `terminal_columns': undefined method `winsize' for nil:NilClass

Issue - State: open - Opened by antonkulaga over 7 years ago - 5 comments

#215 - bioconda install for transrate?

Issue - State: open - Opened by apredeus over 7 years ago - 6 comments

#214 - Gem install failing on Ubuntu 17.04

Issue - State: open - Opened by nickschurch over 7 years ago

#212 - A few changes to Transrate

Pull Request - State: closed - Opened by macmanes over 7 years ago

#211 - How to perform metrics based on reads using single fastq file

Issue - State: closed - Opened by patrick-douglas over 7 years ago - 1 comment

#209 - SNAP Fail to run with 1.0.3

Issue - State: open - Opened by jdeyar almost 8 years ago

#208 - Weird read mapping metrics on version 1.0.3

Issue - State: open - Opened by RuiMMFaria almost 8 years ago - 10 comments

#207 - makeblastdb issues

Issue - State: open - Opened by genizamt almost 8 years ago - 4 comments

#206 - SNAP failed with Transrate v 1.0.3

Issue - State: open - Opened by Jinjie-Duan almost 8 years ago - 8 comments

#205 - After installing transrate via ruby showing syntex errror

Issue - State: closed - Opened by hackerzone85 over 8 years ago - 1 comment

#204 - SNAP failed

Issue - State: closed - Opened by abshah over 8 years ago - 1 comment

#203 - Install transrate in docker image of ubuntu 16.04 / salmon:0.4 error

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

#202 - Dependencies are missing: - salmon (0.6.0)

Issue - State: open - Opened by brunolouro over 8 years ago - 17 comments

#201 - Transrate's salmon parameters associated with "missing" mapped reads mystery

Issue - State: open - Opened by eeflynn over 8 years ago - 4 comments

#200 - Error in snap beta installation

Issue - State: open - Opened by lplough over 8 years ago - 2 comments

#199 - long time to calculate read diagnostics

Issue - State: open - Opened by dcopetti over 8 years ago - 2 comments

#198 - SNAP seed size

Issue - State: open - Opened by alephreish over 8 years ago - 2 comments

#197 - Link to CITATION.md in README

Pull Request - State: closed - Opened by blahah over 8 years ago

#196 - Update citation to Genome Research paper

Pull Request - State: closed - Opened by blahah over 8 years ago

#195 - Read Diagnostics, SNAP failing

Issue - State: closed - Opened by JakeGoodall almost 9 years ago - 1 comment

#194 - Installing dependencies with version 1.0.3

Issue - State: closed - Opened by abshah almost 9 years ago - 1 comment

#193 - Relative pathing doesn't work

Issue - State: closed - Opened by Jorisvansteenbrugge almost 9 years ago - 1 comment

#192 - Example command doesn't work

Issue - State: closed - Opened by simonvh almost 9 years ago - 2 comments

#191 - Possible fix for indexing issue. Was failing to increase locationSiz…

Pull Request - State: closed - Opened by jorvis almost 9 years ago - 1 comment

#190 - SNAP failed

Issue - State: closed - Opened by jwidmann almost 9 years ago - 7 comments

#189 - Transcriptome too large?

Issue - State: closed - Opened by jorvis almost 9 years ago - 20 comments

#188 - File paths must be absolute

Issue - State: closed - Opened by jorvis almost 9 years ago - 2 comments

#187 - --install-deps help message is annoyingly wrong

Issue - State: closed - Opened by ctb almost 9 years ago - 3 comments

#186 - 1.02 downloaded transrate install runs in install directory, not working directory.

Issue - State: closed - Opened by ctb almost 9 years ago - 2 comments
Labels: bug, devops

#185 - transrate stuck in "Calculating comparative metrics" step

Issue - State: open - Opened by IdoBar almost 9 years ago - 9 comments

#184 - transrate "stuck"?

Issue - State: closed - Opened by sjannielefevre almost 9 years ago - 8 comments

#183 - too many 'real' transcripts filtered

Issue - State: open - Opened by macmanes almost 9 years ago - 1 comment

#182 - undefined method `length' for nil:NilClass (NoMethodError)

Issue - State: closed - Opened by johnsolk about 9 years ago - 1 comment
Labels: bug, can't reproduce

#181 - Packaging in salmon (on OSX 10.10.5)

Issue - State: closed - Opened by AndrewIrwin about 9 years ago - 11 comments
Labels: bug, can't reproduce

#180 - Record citations somewhere

Issue - State: open - Opened by blahah about 9 years ago
Labels: enhancement, documentation

#179 - add description for contigs segmented

Issue - State: closed - Opened by macmanes about 9 years ago

#178 - make p_bad_mappings

Issue - State: closed - Opened by macmanes about 9 years ago - 4 comments
Labels: documentation, good first issue

#176 - users confused about metrics to report - write clear guide

Issue - State: open - Opened by blahah about 9 years ago
Labels: enhancement, documentation

#174 - snap-aligner running single-threaded instead of multi-threaded

Issue - State: closed - Opened by KhudyakovLab about 9 years ago - 2 comments
Labels: bug, can't reproduce

#172 - suggested sed to fix assembly fasta header does not work

Issue - State: closed - Opened by johnsolk about 9 years ago - 1 comment

#171 - Account for heterogeneity of the sample by using background distribution of edit distance

Issue - State: open - Opened by blahah about 9 years ago
Labels: enhancement

#170 - Use reference distribution comparison in numerical tests

Issue - State: open - Opened by blahah about 9 years ago
Labels: enhancement

#166 - Allow disabling or caching of contig metrics calculation

Issue - State: open - Opened by ctb over 9 years ago - 1 comment
Labels: enhancement, good first issue

#164 - Installation docs out-of-date wrt --install-deps

Issue - State: closed - Opened by ctb over 9 years ago - 10 comments

#163 - allow gzipped reference

Issue - State: open - Opened by macmanes over 9 years ago - 2 comments
Labels: enhancement, good first issue

#162 - interleaved reads

Issue - State: open - Opened by macmanes over 9 years ago - 9 comments
Labels: enhancement, good first issue

#160 - transrate Debian packaging

Issue - State: open - Opened by mr-c over 9 years ago - 16 comments
Labels: enhancement, devops

#158 - Transrate and how the number of contigs with an ORF is defined

Issue - State: closed - Opened by amabdelhaliem over 9 years ago - 2 comments
Labels: question

#157 - snap fails on files without an fq/fa suffix

Issue - State: open - Opened by camillescott over 9 years ago - 3 comments
Labels: bug

#155 - similar score, very different assembly

Issue - State: open - Opened by macmanes over 9 years ago - 8 comments
Labels: question

#147 - Score database

Issue - State: open - Opened by macmanes over 9 years ago - 2 comments
Labels: longterm, devops, discussion

#141 - Integrate bindeps into release packaging process

Issue - State: closed - Opened by blahah over 9 years ago - 1 comment
Labels: enhancement, devops

#132 - beta3 bug in calculating read diagnostics

Issue - State: closed - Opened by macmanes almost 10 years ago - 5 comments
Labels: bug, can't reproduce

#127 - new Trinity fasta headers causing problems

Issue - State: open - Opened by macmanes about 10 years ago - 7 comments
Labels: documentation

#122 - allow compressed reads as input (fastq.gz, fastq.bz2)

Issue - State: open - Opened by blahah about 10 years ago - 1 comment
Labels: enhancement, good first issue

#114 - add a progress meter and estimate of time remaining

Issue - State: open - Opened by blahah about 10 years ago - 2 comments
Labels: enhancement, good first issue

#107 - Move Cmd to its own gem

Issue - State: open - Opened by blahah over 10 years ago
Labels: enhancement, devops

#97 - More explicit logging with debug option

Issue - State: closed - Opened by blahah over 10 years ago - 2 comments
Labels: enhancement

#78 - visualisation of assembly metrics

Issue - State: open - Opened by blahah over 10 years ago
Labels: enhancement, longterm

#64 - Strand specific option for read alignment

Issue - State: open - Opened by MatthewRalston over 10 years ago
Labels: enhancement, documentation