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
#253 - Linux binary for v1.0.3 cannot be downloaded
Issue -
State: open - Opened by fran-romero-campero 6 months ago
- 2 comments
#252 - Update snap.rb to fix failure to build index
Pull Request -
State: open - Opened by IdoBar 6 months ago
#251 - Transrate FASTQ based run not working
Issue -
State: open - Opened by Gruxxis 10 months ago
- 1 comment
#250 - Compiled repo link is obsolete
Issue -
State: open - Opened by asan-emirsaleh over 1 year ago
#249 - salmon version to be installed by --install-deps=all
Issue -
State: open - Opened by asan-emirsaleh over 1 year ago
#248 - Snap index error
Issue -
State: open - Opened by asan-emirsaleh over 1 year ago
- 3 comments
#247 - salmon: error while loading shared libraries
Issue -
State: open - Opened by Liyong-Zhang over 1 year ago
- 1 comment
#246 - merge assemblies
Issue -
State: open - Opened by ewelinarubin almost 2 years ago
- 1 comment
#245 - Linux download not working v1.0.3
Issue -
State: open - Opened by Tina-L-Nguyen almost 3 years ago
- 1 comment
#244 - Conda installation fails based on 'glibc' dependency issue
Issue -
State: closed - Opened by timslittle almost 3 years ago
- 1 comment
#243 - supported bridges.csv missing from output
Issue -
State: open - Opened by Shabbirm21 about 3 years ago
#242 - Broken link to obtain code
Issue -
State: open - Opened by chrisreidy over 3 years ago
- 1 comment
#241 - weird results (v1.0.3)
Issue -
State: open - Opened by manuelsmendoza about 4 years ago
- 5 comments
#240 - Failed to install-deps
Issue -
State: open - Opened by Gyzele about 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
#237 - [ERROR] 2020-04-22 12:10:41 : ReadMetrics: could not find bam-read in path
Issue -
State: closed - Opened by VaneSGT over 4 years ago
#236 - Depend on salmon 0.7.2
Pull Request -
State: open - Opened by gbrsales over 4 years ago
#235 - SNAP error in Transrate with large dataset
Issue -
State: open - Opened by upendra2020 over 4 years ago
- 1 comment
#234 - Not able to install transrate (ruby error) ?
Issue -
State: open - Opened by sunnyEV over 4 years ago
#233 - Installation error: Error installing transrate-1.0.3.gem ERROR: Failed to build gem native extension
Issue -
State: open - Opened by lychen83 almost 5 years ago
#232 - SNAP error
Issue -
State: open - Opened by zolotarovgl almost 5 years ago
- 1 comment
#231 - MPI implementation
Issue -
State: open - Opened by rafaeltiveron almost 5 years ago
- 1 comment
#230 - Transrate broken and unsupported?
Issue -
State: closed - Opened by Shellfishgene about 5 years ago
- 4 comments
#229 - tpm, eff_count, and coverage all zero in contigs.csv
Issue -
State: open - Opened by matthewabirk over 5 years ago
- 1 comment
#228 - Snap found unmatched read IDs in input fastq files
Issue -
State: open - Opened by elainfl over 5 years ago
- 2 comments
#227 - The solvation of librt.so.1 in Ubuntu 16.04 server
Issue -
State: open - Opened by life404 over 5 years ago
- 2 comments
#226 - transrate in conda project
Issue -
State: closed - Opened by manuelsmendoza over 5 years ago
- 4 comments
#225 - Snap failing due to memory requirements on large transcriptomes
Issue -
State: open - Opened by kvpmulder over 5 years ago
- 2 comments
#224 - Salmon is failing
Issue -
State: open - Opened by sagnikbanerjee15 almost 6 years ago
- 4 comments
#223 - Salmon
Issue -
State: open - Opened by OnlyHigh almost 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 over 6 years ago
#220 - Unexpectedly low `p fragments mapped`
Issue -
State: open - Opened by kmnip over 6 years ago
#219 - Dependencies are missing -salmon (0.6.0)
Issue -
State: open - Opened by Portvin over 6 years ago
- 1 comment
#218 - SNAP failing in v 1.0.3
Issue -
State: open - Opened by ssander5 over 6 years ago
- 5 comments
#217 - Weird read mapping metrics on version 1.0.3
Issue -
State: open - Opened by RuiMMFaria almost 7 years ago
#216 - `terminal_columns': undefined method `winsize' for nil:NilClass
Issue -
State: open - Opened by antonkulaga almost 7 years ago
- 5 comments
#215 - bioconda install for transrate?
Issue -
State: open - Opened by apredeus almost 7 years ago
- 6 comments
#214 - Gem install failing on Ubuntu 17.04
Issue -
State: open - Opened by nickschurch about 7 years ago
#213 - error sched_setaffinity: Invalid argument with transrate v1.0.3
Issue -
State: open - Opened by KhudyakovLab about 7 years ago
#212 - A few changes to Transrate
Pull Request -
State: closed - Opened by macmanes about 7 years ago
#211 - How to perform metrics based on reads using single fastq file
Issue -
State: closed - Opened by patrick-douglas about 7 years ago
- 1 comment
#210 - Salmon (0.6.0) [jointLog] [warning] [Sampler.hpp]: Failed to sample an alignment
Issue -
State: open - Opened by XinpengQi over 7 years ago
- 4 comments
#209 - SNAP Fail to run with 1.0.3
Issue -
State: open - Opened by jdeyar over 7 years ago
#208 - Weird read mapping metrics on version 1.0.3
Issue -
State: open - Opened by RuiMMFaria over 7 years ago
- 10 comments
#207 - makeblastdb issues
Issue -
State: open - Opened by genizamt over 7 years ago
- 4 comments
#206 - SNAP failed with Transrate v 1.0.3
Issue -
State: open - Opened by Jinjie-Duan over 7 years ago
- 8 comments
#205 - After installing transrate via ruby showing syntex errror
Issue -
State: closed - Opened by hackerzone85 almost 8 years ago
- 1 comment
#204 - SNAP failed
Issue -
State: closed - Opened by abshah almost 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 almost 8 years ago
- 2 comments
#202 - Dependencies are missing: - salmon (0.6.0)
Issue -
State: open - Opened by brunolouro about 8 years ago
- 17 comments
#201 - Transrate's salmon parameters associated with "missing" mapped reads mystery
Issue -
State: open - Opened by eeflynn about 8 years ago
- 4 comments
#200 - Error in snap beta installation
Issue -
State: open - Opened by lplough about 8 years ago
- 2 comments
#199 - long time to calculate read diagnostics
Issue -
State: open - Opened by dcopetti about 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 over 8 years ago
- 1 comment
#194 - Installing dependencies with version 1.0.3
Issue -
State: closed - Opened by abshah over 8 years ago
- 1 comment
#193 - Relative pathing doesn't work
Issue -
State: closed - Opened by Jorisvansteenbrugge over 8 years ago
- 1 comment
#192 - Example command doesn't work
Issue -
State: closed - Opened by simonvh over 8 years ago
- 2 comments
#191 - Possible fix for indexing issue. Was failing to increase locationSiz…
Pull Request -
State: closed - Opened by jorvis over 8 years ago
- 1 comment
#190 - SNAP failed
Issue -
State: closed - Opened by jwidmann over 8 years ago
- 7 comments
#189 - Transcriptome too large?
Issue -
State: closed - Opened by jorvis over 8 years ago
- 20 comments
#188 - File paths must be absolute
Issue -
State: closed - Opened by jorvis over 8 years ago
- 2 comments
#187 - --install-deps help message is annoyingly wrong
Issue -
State: closed - Opened by ctb over 8 years ago
- 3 comments
#186 - 1.02 downloaded transrate install runs in install directory, not working directory.
Issue -
State: closed - Opened by ctb over 8 years ago
- 2 comments
Labels: bug, devops
#185 - transrate stuck in "Calculating comparative metrics" step
Issue -
State: open - Opened by IdoBar over 8 years ago
- 9 comments
#184 - transrate "stuck"?
Issue -
State: closed - Opened by sjannielefevre over 8 years ago
- 8 comments
#183 - too many 'real' transcripts filtered
Issue -
State: open - Opened by macmanes over 8 years ago
- 1 comment
#182 - undefined method `length' for nil:NilClass (NoMethodError)
Issue -
State: closed - Opened by johnsolk over 8 years ago
- 1 comment
Labels: bug, can't reproduce
#181 - Packaging in salmon (on OSX 10.10.5)
Issue -
State: closed - Opened by AndrewIrwin over 8 years ago
- 11 comments
Labels: bug, can't reproduce
#180 - Record citations somewhere
Issue -
State: open - Opened by blahah over 8 years ago
Labels: enhancement, documentation
#179 - add description for contigs segmented
Issue -
State: closed - Opened by macmanes almost 9 years ago
#178 - make p_bad_mappings
Issue -
State: closed - Opened by macmanes almost 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 almost 9 years ago
Labels: enhancement, documentation
#174 - snap-aligner running single-threaded instead of multi-threaded
Issue -
State: closed - Opened by KhudyakovLab almost 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 almost 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 almost 9 years ago
Labels: enhancement
#170 - Use reference distribution comparison in numerical tests
Issue -
State: open - Opened by blahah almost 9 years ago
Labels: enhancement
#166 - Allow disabling or caching of contig metrics calculation
Issue -
State: open - Opened by ctb almost 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 almost 9 years ago
- 10 comments
#163 - allow gzipped reference
Issue -
State: open - Opened by macmanes almost 9 years ago
- 2 comments
Labels: enhancement, good first issue
#162 - interleaved reads
Issue -
State: open - Opened by macmanes almost 9 years ago
- 9 comments
Labels: enhancement, good first issue
#160 - transrate Debian packaging
Issue -
State: open - Opened by mr-c about 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 about 9 years ago
- 2 comments
Labels: question
#157 - snap fails on files without an fq/fa suffix
Issue -
State: open - Opened by camillescott about 9 years ago
- 3 comments
Labels: bug
#155 - similar score, very different assembly
Issue -
State: open - Opened by macmanes about 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 over 9 years ago
- 5 comments
Labels: bug, can't reproduce
#127 - new Trinity fasta headers causing problems
Issue -
State: open - Opened by macmanes over 9 years ago
- 7 comments
Labels: documentation
#122 - allow compressed reads as input (fastq.gz, fastq.bz2)
Issue -
State: open - Opened by blahah over 9 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 almost 10 years ago
- 2 comments
Labels: enhancement, good first issue
#107 - Move Cmd to its own gem
Issue -
State: open - Opened by blahah almost 10 years ago
Labels: enhancement, devops
#97 - More explicit logging with debug option
Issue -
State: closed - Opened by blahah almost 10 years ago
- 2 comments
Labels: enhancement
#78 - visualisation of assembly metrics
Issue -
State: open - Opened by blahah about 10 years ago
Labels: enhancement, longterm
#64 - Strand specific option for read alignment
Issue -
State: open - Opened by MatthewRalston about 10 years ago
Labels: enhancement, documentation
#58 - cli: --print-commands
Issue -
State: closed - Opened by blahah about 10 years ago
- 3 comments
Labels: enhancement