AuReMe metage2metabo issues

AuReMe / metage2metabo

From annotated genomes to metabolic screening in large scale microbiotas

https://metage2metabo.readthedocs.io

GNU Lesser General Public License v3.0

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issues

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M2M workflow and mincom

#64 ggmirandac opened 4 weeks ago
1
fix typos and clarify some sentences

#63 hindrek closed 1 month ago
1
M2M fix missing keys in comm_scopes json.

#62 ArnaudBelcour closed 5 months ago
0
Fix issue 22

#61 ArnaudBelcour closed 7 months ago
0
When using `--pwt-xml`, the xml files extracted from Pathway Tools can be incompatible with python-libsbml.

#60 ArnaudBelcour closed 7 months ago
1
Fix issue #55: sanitize extraction of tar file

#59 ArnaudBelcour closed 8 months ago
0
Do not allow abbreviation in command arguments (issue #54).

#58 ArnaudBelcour closed 8 months ago
0
53 individual scopes include seeds even if non producible or absent from the gsmns

#57 cfrioux closed 9 months ago
0
gff file format problem while running m2m recon

#56 gpchoupichou opened 9 months ago
1
Sanitize use of tarfile extractall.

#55 ArnaudBelcour closed 8 months ago
1
Do not allow abbreviation in command arguments.

#54 ArnaudBelcour closed 8 months ago
1
Individual scopes include seeds even if non producible or absent from the GSMNs

#53 cfrioux closed 9 months ago
3
mpwt could not find the version of Pathway Tools

#52 Choaro opened 1 year ago
1
How to prepare inputs for metage2metabo

#51 LiZhihua1982 closed 9 months ago
3
Install metage2metabo problem

#50 LiZhihua1982 closed 9 months ago
5
Fix html powergraph creation

#49 ArnaudBelcour closed 1 year ago
0
[Question] Where can I find seed files?

#48 jolespin closed 9 months ago
4
No /home/chencong/.ncbirc file, please fix it before using the program

#47 ChenCongZ closed 9 months ago
5
CRITICAL:metage2metabo.m2m.reconstruction:Something went wrong running Pathway Tools. See the log file in /home/chencong/output3/pgdb_log/log_error.txt

#46 ChenCongZ closed 1 year ago
6
Error with analysis graph when using taxon_id

#45 KDeaton closed 1 year ago
5
CVE-2007-4559 Patch

#44 TrellixVulnTeam closed 8 months ago
1
m2m recon not working with gbff file inputs

#43 alsmadin01 closed 1 year ago
4
m2m 1.5.1

#42 ArnaudBelcour closed 2 years ago
0
m2m_analysis powergraph not working as expected

#41 alsmadin01 closed 2 years ago
27
Update README.md

#40 cfrioux closed 2 years ago
0
Non optimal powergraph visualisation

#39 ArnaudBelcour opened 2 years ago
2
Compute deadend and orphan metabolites

#38 ArnaudBelcour opened 2 years ago
0
Issue with pathway tools API limitation and PGDB entries verification

#37 Adifo closed 2 years ago
4
A better focus on the host metabolism when a host is provided

#36 cfrioux opened 2 years ago
1
Multiple errors when running test data

#35 DafniGi closed 2 years ago
7
I have the following problems when running the t2d_m2m_target_producers.R file:

#34 ChenCongZ closed 2 years ago
8
Revert "Test CI with newer versions of Python"

#33 cfrioux closed 2 years ago
0
A few process questions

#32 KDeaton closed 2 years ago
4
I'm terribly sorry, but I can't solve it by trying many methods. I'm looking for your help.

#31 ChenCongZ closed 2 years ago
0
Progress problem

#30 ChenCongZ closed 2 years ago
4
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

#29 ChenCongZ closed 2 years ago
0
Hi

#28 ChenCongZ closed 2 years ago
0
Test CI with newer versions of Python

#27 cfrioux closed 2 years ago
0
m2m_analysis - deal with powergrasp config file creation when launching multiple runs

#26 ArnaudBelcour opened 2 years ago
0
UnicodeDecodeError when running m2m_analysis with Singularity

#25 cfrioux closed 7 months ago
2
"Can't connect to X11 window server using..." m2m_analysis

#24 cfrioux closed 7 months ago
2
m2m_analysis : ignore unproducible targets

#23 cfrioux closed 7 months ago
3
m2m_analysis - deal with empty last row when reading taxon_id

#22 cfrioux closed 7 months ago
1
Create a list of targets for the content of the community metabolic potential

#21 cfrioux closed 7 months ago
3
Producibility_targets file is not created when `m2m mincom` is called

#20 cfrioux closed 8 months ago
1
Producibility_targets.json does not include essential and alterative symbiont list

#19 cfrioux closed 7 months ago
1
Help with creating seed file

#18 choon-sim closed 2 years ago
4
Error during recon: XML not well formed

#17 KDeaton closed 3 years ago
2
New GenBank file format

#16 KDeaton closed 3 years ago
1
metabolic objective

#15 choon-sim closed 3 years ago
2