hallamlab metapathways2 issues

hallamlab / metapathways2

MetaPathways v2.0: A master-worker model for environmental Pathway/Genome Database construction on grids and clouds

http://hallam.microbiology.ubc.ca/MetaPathways/

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issues

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template_config.txt forces the appending of MP install directory to executable paths

#103 katharinedickson opened 3 years ago
0
Failed to run Pathologic

#102 TarsLi opened 4 years ago
0
Wrong orfs annotation scoring results

#101 kfiedoruk opened 5 years ago
0
MetaPathways 2.5.2 Fails at Running PathoLogic Step

#100 JSkar opened 5 years ago
0
missing --out-ptinput option in MetaPathways_create_genbank.py

#99 mthang opened 6 years ago
0
command line metapathways fails to annotate

#98 blancaverag closed 7 years ago
3
Failed to Format LSURef

#97 GiangLeN closed 7 years ago
0
Documentation for MLtreemap

#96 taltman closed 7 years ago
1
Failure to annotate (KeyError: 'partial')

#95 jessieluolab closed 7 years ago
4
failure to annotate metagenome

#94 ademenez closed 7 years ago
1
Installation of metapathways on linux cluster

#93 ademenez closed 7 years ago
1
Issue with displaying results in GUI in MP v. 2.5.1.

#92 GlassLabGT closed 7 years ago
6
MP does not respect the Unix exit code convention

#91 taltman closed 7 years ago
1
Truncating nucleotide sequences with ambiguous nucleotides

#90 joshamilton closed 7 years ago
2
Current RPKM script has major bugs

#89 cmorganl closed 7 years ago
2
How to analyse a large dataset remotelly

#88 ademenez closed 7 years ago
4
MP doesn't create incrementing locus ID for contig trna genes

#87 taltman closed 7 years ago
1
MP2 happily reports, "THE END", but blastp keeps chugging away

#86 taltman closed 7 years ago
1
MP2 doesn't recognize large formatted DBs due to chunk files

#85 taltman closed 7 years ago
1
Shouldn't MP2 be using FragGeneScanPlus?

#84 taltman closed 7 years ago
1
MP2 Should utilize all CPUs when processing a set of samples, and spare CPUs are available

#83 taltman closed 7 years ago
1
MP2: "BLAST Database error: Could not find volume or alias file"

#82 taltman closed 7 years ago
1
MP2 should utilize all CPUs in database indexing phase

#81 taltman closed 7 years ago
1
MP2 should just use the OS path for finding executables

#80 taltman closed 7 years ago
1
Makefile for executables/sources needs updating

#79 taltman closed 7 years ago
3
Test dataset

#78 gwilymh closed 7 years ago
1
The bundled metacyc-v5-2011-10-21 does not seem to 'work'

#77 gwilymh closed 7 years ago
5
Addition of "/" in DB path

#76 driscolc closed 9 years ago
3
Fedora, Centos, Redhat?

#75 nmb85 closed 9 years ago
1
Problem with Grid setup

#74 rpelicae closed 7 years ago
1
Generation of stats table for GreenGenes Blast results silently fails

#73 taltman closed 7 years ago
1
rRNA Annotations do not make it into the ePGDB

#72 taltman closed 7 years ago
1
Some contigs not present in functional_and_taxonomic_table.txt

#71 taltman closed 7 years ago
1
Detection of Eukaryotic genes seems not to work

#70 taltman closed 7 years ago
4
Functional database installation

#69 ctSkennerton closed 7 years ago
5
Problems installing python modules

#68 ctSkennerton closed 9 years ago
2
Link to databases broken

#67 ctSkennerton closed 9 years ago
2
rRNA sequence FASTA export produces rDNA

#66 taltman closed 7 years ago
1
Missing documentation on how to install ML-TreeMap

#65 taltman closed 7 years ago
1
Bad annotation merging method

#64 taltman closed 7 years ago
3
MP doesn't tell PTools to run the Transport Inference Parser

#63 taltman closed 7 years ago
1
MP shouldn't cram all annotations into single line on PF file

#62 taltman closed 7 years ago
1
MP not using MetaCyc annotations correctly in *.pf file

#61 taltman closed 7 years ago
1
Enhancement: Downloader scripts

#60 taltman closed 7 years ago
1
RefSeq FTP URL is not at right level

#59 taltman closed 7 years ago
2
Incorrect LCA computation

#58 taltman closed 7 years ago
8
Documentation on grid setup

#57 rpelicae closed 7 years ago
1
PathoLogic error opaque to user

#56 taltman closed 7 years ago
18
libQt5PrintSupport.so.5: cannot open shared object file: No such file or directory

#55 nielshanson closed 9 years ago
1
MP provides no way to specify the OrgID for the ePGDB

#54 taltman closed 7 years ago
3