issues
search
franciscozorrilla
/
metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
https://franciscozorrilla.github.io/metaGEM/
MIT License
203
stars
42
forks
source link
issues
Newest
Newest
Most commented
Recently updated
Oldest
Least commented
Least recently updated
Issue running concoct with crossMapParallel pathway
#57
jorgeln0
closed
3 years ago
7
documentation on running metaGEM using user-generated contig assemblies
#56
zoey-rw
closed
1 year ago
3
bug: binReassemble implementation suboptimal without --parallel flag
#55
franciscozorrilla
closed
3 years ago
0
feat: Check if files/folders exist in tmpdir before copying them within Snakefile rules
#54
franciscozorrilla
closed
2 years ago
0
bug: maxbinCross rule does not use multiple threads
#53
franciscozorrilla
closed
3 years ago
0
Update needed to modelVis rule for models reconstructed using CarveMe version>=1.5.0
#52
shreyanshumale
opened
3 years ago
1
feat: Add optional feature to automate download of user-defined dataset
#51
franciscozorrilla
closed
2 years ago
0
[OGE scheduler] Problem with the model reconstruction (carveme) step
#50
shreyanshumale
closed
3 years ago
5
sbatch: not found Error submitting jobscript (exit code 127):
#49
kingtom2016
closed
3 years ago
2
'compositionVis' , 'abundanceVis' and 'taxonomyVis' rule errors
#48
shreyanshumale
closed
3 years ago
2
Someone can provide a virtual disk or something to run data directly?
#47
kingtom2016
closed
3 years ago
1
feat: Option for users to upload their data to google colab
#46
franciscozorrilla
closed
2 years ago
0
bug: problems with GTDBTk, small correction in the snakefile needed
#45
shreyanshumale
closed
3 years ago
2
How to run on a cluster without workload manager
#44
slambrechts
closed
3 years ago
4
error while running env_setup.sh script:
#43
slambrechts
closed
3 years ago
8
feat: Implement complementary pre-assembly binning for additional MAG generation
#42
franciscozorrilla
closed
2 years ago
0
feat: add rule that identifies potentially novel genomes from MAGs
#35
franciscozorrilla
closed
2 years ago
2
Rule assemblyVis has commented out two relevant lines
#34
matrs
closed
3 years ago
1
feat: use snakemake integrated conda feature to annotate jobs
#33
franciscozorrilla
closed
2 years ago
0
bug: r-gridextra missing from metagem environment
#32
franciscozorrilla
closed
3 years ago
3
feat: Implement optional modification to loop metaWRAP refinement + reassembly
#31
franciscozorrilla
closed
2 years ago
2
feat: create task/sample specific folder within each job that uses scratch dir
#30
franciscozorrilla
closed
2 years ago
1
feat: Add bashplotlib to stats task for quick visualization on the command line
#29
franciscozorrilla
closed
2 years ago
1
feat: Add KneadData as optional pre-processing of raw data
#28
franciscozorrilla
closed
2 years ago
1
[Question] Option to filter host's DNA
#27
matrs
closed
3 years ago
2
error in rule megahit when running two or more jobs in parallel
#26
matrs
closed
3 years ago
4
Create two new metaGEM.sh tasks: check and stats
#25
franciscozorrilla
closed
3 years ago
1
Is it common that only about 30 MAGs of high quality were obtained from one metagenome sample?
#24
hongzhonglu
closed
3 years ago
23
Develop and expand repo wiki
#23
franciscozorrilla
closed
3 years ago
1
feat: Add crossMap3-based method rules to metaGEM.sh parser
#22
franciscozorrilla
closed
3 years ago
1
Add scratchdir/tmpdir folder in config file
#21
franciscozorrilla
closed
3 years ago
1
Question about generating "depth.txt" for metabat2
#20
hongzhonglu
closed
3 years ago
5
Create LICENSE
#19
franciscozorrilla
closed
3 years ago
0
feat: Add cluster workload manager specific flags for metaGEM.sh parser to handle non-slurm cases
#18
franciscozorrilla
closed
2 years ago
3
Add flag to metaGEM.sh parser to allow users to force certain jobs/tasks to be submitted locally
#17
franciscozorrilla
closed
3 years ago
1
Running metaGEM.sh parser locally
#16
karinedurand
closed
3 years ago
9
Have you metadata for the GEMs from gut
#15
hongzhonglu
closed
3 years ago
3
feat: Add optional feature to separate contigs after assembly
#14
franciscozorrilla
closed
2 years ago
0
why use gap filling with carveme
#13
vrmarcelino
closed
3 years ago
2
Regarding usage, installing CPLEX & CarveMe
#12
ShailNair
closed
3 years ago
14
Dev update: pangenome analysis, drep, coassembly test, abundance fix
#11
franciscozorrilla
closed
4 years ago
0
Big PR adding new snakefile for single end datasets and reimplemented cross mapping of samples for all binners using bwa
#10
franciscozorrilla
closed
4 years ago
0
Added main figure
#9
franciscozorrilla
closed
4 years ago
0
Many small improvements and standardizations (read commit history for specific details)
#8
franciscozorrilla
closed
4 years ago
0
feat: added visualization rules to Snakefile, refactor: moved from python2 to python3, refactor: many small improvements to parser file
#7
franciscozorrilla
closed
4 years ago
0
refactor: metaBAGpipes.sh only runs parse() funtion if arguments are provided
#6
franciscozorrilla
closed
5 years ago
0
fix: Remove duplicate file metaparser.sh
#5
franciscozorrilla
closed
5 years ago
0
rename metaparser to metaBAGpipes
#4
franciscozorrilla
closed
5 years ago
0
feat: add metaparse.sh script to simplify user experience/interface
#3
franciscozorrilla
closed
5 years ago
0
Dev
#2
franciscozorrilla
closed
5 years ago
0
Previous
Next