ccdmb/predector issues and pull requests

#95 - phobius not found

Issue - State: open - Opened by vappiah 4 months ago - 3 comments

#94 - New subversion of signalP 6.0 (g -> h), new version of deeploc (1.0 -> 2.0), difference in phobius (.tar.gz -> .tgz)

Issue - State: open - Opened by markusHaferkamp 4 months ago - 2 comments

#93 - Xboost BUG:

Issue - State: open - Opened by MmasterT over 1 year ago - 4 comments
Labels: bug

#92 - BUG: Signal4.1 segfaults using docker

Issue - State: open - Opened by krostifangers over 1 year ago - 7 comments
Labels: bug

#91 - Appoplast conflict

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

#90 - Dev

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

#89 - Devel

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

#88 - FEATURE REQUEST: dbcan 11

Issue - State: closed - Opened by darcyabjones over 2 years ago - 1 comment
Labels: enhancement

#87 - BUG: Deepredeff output is empty

Issue - State: closed - Opened by darcyabjones over 2 years ago - 8 comments
Labels: bug

#86 - FEATURE REQUEST: DeepLoc2 now available to download.

Issue - State: open - Opened by darcyabjones over 2 years ago
Labels: enhancement

#85 - Copy result files to results folder instead of linking

Pull Request - State: closed - Opened by IdoBar over 2 years ago - 4 comments

#84 - BUG: result files point to dead links when cleanup = true (or after running nextflow clean -f)

Issue - State: closed - Opened by IdoBar over 2 years ago - 5 comments
Labels: bug

#83 - New release

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

#82 - BUG: Names of all my proteins in tsv file are "."

Issue - State: closed - Opened by thdurand4 over 2 years ago - 8 comments
Labels: bug

#81 - BUG:Installation error ImportError: cannot import name 'Protocol'

Issue - State: closed - Opened by Unalibun over 2 years ago - 3 comments
Labels: bug

#80 - Remove pinning of python to v3.6

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

#79 - Installation fails when testing DeepLoc

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

#78 - BUG:

Issue - State: closed - Opened by darcyabjones over 2 years ago - 1 comment
Labels: bug

#77 - BUG: Mamba environment installation problem

Issue - State: closed - Opened by Hoberti over 2 years ago - 5 comments
Labels: bug

#76 - 1.2.5 tag

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

#75 - BUG: Installer silently fails while registering signalp3

Issue - State: closed - Opened by darcyabjones almost 3 years ago - 1 comment
Labels: bug

#74 - Merging in changes for 1.2.3

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

#73 - FEATURE REQUEST: Handle tar de-compression specification properly in conda register scripts

Issue - State: closed - Opened by darcyabjones almost 3 years ago - 1 comment
Labels: enhancement

#70 - BUG: Problem with "Registering source file signalp-3.0.Linux.tar.Z"

Issue - State: closed - Opened by a-velt almost 3 years ago - 4 comments
Labels: bug

#69 - BUG: Process `signalp_v6 (1)` terminated with an error exit status (1)

Issue - State: closed - Opened by tdymc almost 3 years ago - 5 comments
Labels: bug

#68 - BUG: Conda registration of signalp-4.1g.Linux.tar.gz & phobius101_linux.tar.gz

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

#67 - Update to use SP 6.0c

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

#66 - Update to work with SignalP 6.0b

Pull Request - State: closed - Opened by darcyabjones about 3 years ago

#65 - FEATURE REQUEST: Add a check to `install.sh` and conda register scripts to check for correct SignalP6 model

Issue - State: closed - Opened by darcyabjones about 3 years ago - 3 comments
Labels: enhancement

#64 - build docker container failed

Issue - State: closed - Opened by zengtian2680 about 3 years ago - 6 comments
Labels: documentation, question

#62 - FEATURE REQUEST: Diversify the test set a bit

Issue - State: closed - Opened by darcyabjones about 3 years ago - 1 comment
Labels: enhancement, good first issue

#61 - Update output.md

Pull Request - State: closed - Opened by fmobegi about 3 years ago - 1 comment

#60 - Update output.md

Pull Request - State: closed - Opened by fmobegi about 3 years ago - 1 comment

#59 - The ranking description of outputs should be a table.

Issue - State: closed - Opened by darcyabjones about 3 years ago - 1 comment
Labels: documentation, good first issue, help wanted

#58 - FEATURE REQUEST: Use GPUs for tasks that can utilise them.

Issue - State: open - Opened by darcyabjones about 3 years ago - 1 comment
Labels: enhancement

#56 - FEATURE REQUEST: Option to not run unnecessary slow tools

Issue - State: closed - Opened by darcyabjones about 3 years ago - 1 comment
Labels: enhancement

#55 - BUG: SignalP4 segfaults using conda in WSL2

Issue - State: open - Opened by darcyabjones about 3 years ago
Labels: bug

#54 - BUG: Downloading Pfam-A fails. Connection time out.

Issue - State: closed - Opened by darcyabjones about 3 years ago - 3 comments
Labels: bug

#52 - Deepsig fails with missing tensorflow module

Issue - State: closed - Opened by fmobegi about 3 years ago - 12 comments
Labels: bug

#51 - SignalP6 threadlock

Issue - State: closed - Opened by fmobegi about 3 years ago - 2 comments

#50 - FEATURE REQUEST: Look into integrating post-processing information (e.g. Kex2)

Issue - State: closed - Opened by darcyabjones about 3 years ago - 1 comment
Labels: enhancement

#49 - BUG: SignalP 6 too slow on Supercomputer.

Issue - State: closed - Opened by darcyabjones over 3 years ago - 1 comment
Labels: bug

#48 - Dev

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

#47 - FEATURE REQUEST: Please add Prediction result to the *-ranked.tsv

Issue - State: closed - Opened by xizhesun over 3 years ago - 2 comments
Labels: enhancement

#46 - about the TM domain prediction

Issue - State: open - Opened by xizhesun over 3 years ago - 4 comments

#45 - FEATURE REQUEST: secretomeP

Issue - State: closed - Opened by xizhesun over 3 years ago - 3 comments
Labels: enhancement

#44 - BUG: effectorp_v2 error when Test the pipeline

Issue - State: closed - Opened by xizhesun over 3 years ago - 11 comments
Labels: bug

#43 - FEATURE REQUEST: signalP6.0 support

Issue - State: closed - Opened by xizhesun over 3 years ago - 5 comments
Labels: enhancement

#42 - effectorp3.0 support

Issue - State: closed - Opened by xizhesun over 3 years ago - 4 comments
Labels: enhancement

#41 - FEATURE REQUEST: Sanitise PHI-base input

Issue - State: closed - Opened by darcyabjones over 3 years ago - 2 comments
Labels: enhancement

#40 - BUG: active_site.dat.gz not downloadable anymore

Issue - State: closed - Opened by JWDebler over 3 years ago - 10 comments
Labels: bug

#39 - BUG: deepsig error

Issue - State: closed - Opened by JWDebler over 3 years ago - 2 comments
Labels: bug

#38 - FEATURE REQUEST: Add support for Effectorp3

Issue - State: closed - Opened by darcyabjones over 3 years ago - 1 comment
Labels: enhancement

#37 - FEATURE REQUEST: Incorporate deepredeff into pipeline

Issue - State: closed - Opened by darcyabjones almost 4 years ago - 2 comments
Labels: enhancement

#36 - BUG: docker (long install) test fails

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

#35 - BUG: conda test crashes

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

#34 - BUG: Singularity build fails

Issue - State: closed - Opened by JWDebler over 4 years ago - 9 comments
Labels: bug

#33 - BUG: docker build crashes

Issue - State: closed - Opened by JWDebler over 4 years ago - 2 comments
Labels: bug

#32 - Add check for filename uniqueness

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: enhancement

#31 - BUG: Theano (deeploc) heaps of stuff writes to ~/.theano

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: bug

#30 - BUG: SignalP3-NN fails for long sequences.

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: bug

#29 - Add check for WSL to install.sh

Issue - State: open - Opened by darcyabjones over 4 years ago

#28 - Add example command to run tests for install.sh

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment

#27 - Look into automatically downloading PHIbase

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: help wanted

#26 - Extract information from PHI-Base matches

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: enhancement, help wanted

#25 - New docs section: configuring nextflow and running on supercomputers.

Issue - State: open - Opened by darcyabjones over 4 years ago
Labels: documentation, help wanted

#24 - New docs section: Extended intallation information

Issue - State: closed - Opened by darcyabjones over 4 years ago - 2 comments
Labels: documentation, help wanted

#23 - New documentation page: Pipeline output.

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: documentation, good first issue, help wanted

#22 - Implement effector classification, clustering, and ranking strategy

Issue - State: closed - Opened by darcyabjones over 4 years ago - 3 comments
Labels: enhancement

#21 - Add a wrapper script for building the environment

Issue - State: closed - Opened by darcyabjones over 4 years ago - 1 comment
Labels: enhancement, help wanted

#20 - Conda register scripts should report proper errors if they fail.

Issue - State: open - Opened by darcyabjones over 4 years ago
Labels: enhancement

#19 - Dsl2

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

#18 - Slight tidyup of James' commit

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