AuReMe/metage2metabo issues and pull requests

#64 - M2M workflow and mincom

Issue - State: open - Opened by ggmirandac 3 months ago - 1 comment

#63 - fix typos and clarify some sentences

Pull Request - State: closed - Opened by hindrek 3 months ago - 1 comment

#62 - M2M fix missing keys in comm_scopes json.

Pull Request - State: closed - Opened by ArnaudBelcour 8 months ago

#61 - Fix issue 22

Pull Request - State: closed - Opened by ArnaudBelcour 9 months ago

#60 - When using `--pwt-xml`, the xml files extracted from Pathway Tools can be incompatible with python-libsbml.

Issue - State: closed - Opened by ArnaudBelcour 10 months ago - 1 comment

#59 - Fix issue #55: sanitize extraction of tar file

Pull Request - State: closed - Opened by ArnaudBelcour 11 months ago

#58 - Do not allow abbreviation in command arguments (issue #54).

Pull Request - State: closed - Opened by ArnaudBelcour 11 months ago

#57 - 53 individual scopes include seeds even if non producible or absent from the gsmns

Pull Request - State: closed - Opened by cfrioux 11 months ago

#56 - gff file format problem while running m2m recon

Issue - State: open - Opened by gpchoupichou 11 months ago - 1 comment

#55 - Sanitize use of tarfile extractall.

Issue - State: closed - Opened by ArnaudBelcour 11 months ago - 1 comment

#54 - Do not allow abbreviation in command arguments.

Issue - State: closed - Opened by ArnaudBelcour 11 months ago - 1 comment

#53 - Individual scopes include seeds even if non producible or absent from the GSMNs

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

#52 - mpwt could not find the version of Pathway Tools

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

#51 - How to prepare inputs for metage2metabo

Issue - State: closed - Opened by LiZhihua1982 over 1 year ago - 3 comments

#50 - Install metage2metabo problem

Issue - State: closed - Opened by LiZhihua1982 over 1 year ago - 5 comments

#49 - Fix html powergraph creation

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

#48 - [Question] Where can I find seed files?

Issue - State: closed - Opened by jolespin over 1 year ago - 4 comments

#47 - No /home/chencong/.ncbirc file, please fix it before using the program

Issue - State: closed - Opened by ChenCongZ almost 2 years ago - 5 comments

#46 - CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt

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

#45 - Error with analysis graph when using taxon_id

Issue - State: closed - Opened by KDeaton about 2 years ago - 5 comments

#44 - CVE-2007-4559 Patch

Pull Request - State: closed - Opened by TrellixVulnTeam about 2 years ago - 1 comment

#43 - m2m recon not working with gbff file inputs

Issue - State: closed - Opened by alsmadin01 about 2 years ago - 4 comments

#42 - m2m 1.5.1

Pull Request - State: closed - Opened by ArnaudBelcour about 2 years ago

#41 - m2m_analysis powergraph not working as expected

Issue - State: closed - Opened by alsmadin01 about 2 years ago - 27 comments

#40 - Update README.md

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

#39 - Non optimal powergraph visualisation

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

#38 - Compute deadend and orphan metabolites

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

#37 - Issue with pathway tools API limitation and PGDB entries verification

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

#36 - A better focus on the host metabolism when a host is provided

Issue - State: open - Opened by cfrioux over 2 years ago - 1 comment
Labels: enhancement

#35 - Multiple errors when running test data

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

#34 - I have the following problems when running the t2d_m2m_target_producers.R file:

Issue - State: closed - Opened by ChenCongZ almost 3 years ago - 8 comments

#33 - Revert "Test CI with newer versions of Python"

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

#32 - A few process questions

Issue - State: closed - Opened by KDeaton almost 3 years ago - 4 comments

#31 - I'm terribly sorry, but I can't solve it by trying many methods. I'm looking for your help.

Issue - State: closed - Opened by ChenCongZ almost 3 years ago

#30 - Progress problem

Issue - State: closed - Opened by ChenCongZ almost 3 years ago - 4 comments

#29 - Hi，I'm trying to run your pipeline but I had an error. Do you have any idea how can I solve this? I'm leaving here the input and outputs.Thank you very much

Issue - State: closed - Opened by ChenCongZ almost 3 years ago

#28 - Hi

Issue - State: closed - Opened by ChenCongZ almost 3 years ago

#27 - Test CI with newer versions of Python

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

#26 - m2m_analysis - deal with powergrasp config file creation when launching multiple runs

Issue - State: open - Opened by ArnaudBelcour about 3 years ago
Labels: enhancement

#25 - UnicodeDecodeError when running m2m_analysis with Singularity

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

#24 - "Can't connect to X11 window server using..." m2m_analysis

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

#23 - m2m_analysis : ignore unproducible targets

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

#22 - m2m_analysis - deal with empty last row when reading taxon_id

Issue - State: closed - Opened by cfrioux about 3 years ago - 1 comment

#21 - Create a list of targets for the content of the community metabolic potential

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

#20 - Producibility_targets file is not created when `m2m mincom` is called

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

#19 - Producibility_targets.json does not include essential and alterative symbiont list

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

#18 - Help with creating seed file

Issue - State: closed - Opened by choon-sim about 3 years ago - 4 comments

#17 - Error during recon: XML not well formed

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

#16 - New GenBank file format

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

#15 - metabolic objective

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

#14 - Oog.jar no longer available at link

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

#13 - Error for teste with PathoLogic subprocess, return code: 255

Issue - State: closed - Opened by Lucas-Maciel over 3 years ago - 8 comments

#12 - Powergraph labels

Issue - State: closed - Opened by aassie almost 4 years ago - 3 comments

#11 - Issue during installation with Python 3.8.

Issue - State: closed - Opened by ArnaudBelcour about 4 years ago - 1 comment
Labels: bug

#10 - KeyError 'Producible' when running test data

Issue - State: closed - Opened by DennyPopp about 4 years ago - 5 comments

#9 - Ugly exit when target sbml file has empty metabolites

Issue - State: closed - Opened by cfrioux about 4 years ago
Labels: bug

#8 - Error running iscope -- Something went wrong running Menetools

Issue - State: closed - Opened by aassie over 4 years ago - 14 comments

#7 - Non-caught error in mincom if target sbml is not ok

Issue - State: closed - Opened by cfrioux about 5 years ago - 3 comments
Labels: enhancement

#6 - Add m2m_analysis

Pull Request - State: closed - Opened by ArnaudBelcour about 5 years ago

#5 - Singularity recipe uses python3.5 while clyngor requires a more recent version

Issue - State: closed - Opened by cfrioux over 5 years ago
Labels: bug

#4 - Error with test data.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug

#3 - Enable the use of latest versions of dependencies

Pull Request - State: closed - Opened by cfrioux over 5 years ago

#2 - Issue with pyasp.

Issue - State: closed - Opened by ArnaudBelcour over 5 years ago - 1 comment
Labels: bug

#1 - New structure

Pull Request - State: closed - Opened by cfrioux over 5 years ago

GitHub / AuReMe/metage2metabo issues and pull requests