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hallamlab
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MetaPathways
A modular pipeline for constructing Pathway/Genome Databases from environmental sequence information
http://hallam.microbiology.ubc.ca/MetaPathways
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LCA*
#38
ariahahn
closed
9 years ago
0
problem running Gblocks
#37
danvso
closed
7 years ago
2
Step 11 (annotate gff files) error
#36
maepz
closed
7 years ago
3
Step 15: EOF file error.
#35
sunitj
closed
7 years ago
5
Which files from the KEGG database are needed?
#34
nielshanson
closed
10 years ago
0
refseq-names.txt file is missing
#33
xapple
closed
7 years ago
7
Preprocessing alters sequences
#32
xapple
closed
11 years ago
3
Step 15: Create PGDB not working
#31
xapple
closed
11 years ago
2
Can't skip preprocessing
#30
xapple
closed
7 years ago
2
Arbitrary Limit in MetaPathways_filter_input.py
#29
nielshanson
closed
11 years ago
0
Sequences in Pathway Tools are not correct
#28
nielshanson
closed
11 years ago
0
Implement LAST as an alternative to blastp
#27
nielshanson
closed
11 years ago
0
ML-TreeMap results added to the functional and taxonomic table.
#26
nielshanson
closed
11 years ago
0
over-submission issue on orcinus.westgrid.ca
#25
nielshanson
closed
11 years ago
0
Look into issue why some ML-TreeMap figures are not being produced
#24
nielshanson
closed
11 years ago
0
annotated .gbk input not parsed to ptools input
#23
nielshanson
closed
11 years ago
0
daemon script under-submitting jobs
#22
nielshanson
closed
11 years ago
0
blastp doesn't work on some grid machines
#21
nielshanson
closed
11 years ago
0
New Options for the Grid
#20
nielshanson
closed
11 years ago
0
Distrubute ML-TreeMap RAxML calculations
#19
kishori82
closed
7 years ago
0
Pull list of pathways and reactions from created PGDBs
#18
nielshanson
closed
11 years ago
0
Gathering rRNA stats: correct number of rRNA sequences?
#17
nielshanson
closed
11 years ago
1
Double check the rRNA BLAST, rewriting over results due to SSU and LSU DB names
#16
nielshanson
closed
11 years ago
1
Percent completed bar has some funky behaviour.
#15
hallamlab
closed
11 years ago
0
Not sure if the grid likes dots (.) in filenames
#14
hallamlab
closed
11 years ago
1
Grid does not consolidate results... sometimes
#13
hallamlab
closed
11 years ago
0
Wierd stuff on the output
#12
hallamlab
closed
11 years ago
0
input/output & gird confusion
#11
hallamlab
closed
11 years ago
1
Seems to do quality check step every time...
#10
hallamlab
closed
11 years ago
1
MetaPath to MetaPathways and other namespace changes
#9
hallamlab
closed
11 years ago
0
MLTreeMap not creating images in mltreemap/tables_and_figures/
#8
hallamlab
closed
11 years ago
0
Truncate long names (> 40 characters) of PGDBs
#7
hallamlab
closed
11 years ago
0
Summarize KEGG and CO distributions from a given .gff or .gbk file with annotations
#6
hallamlab
closed
11 years ago
0
RNA genes added to the .pf file
#5
hallamlab
closed
11 years ago
0
Parameter file: 16s_rRNA to rRNA
#4
hallamlab
closed
11 years ago
1
Pathway Tools directories may have to be added to a user's $PATH variable as part of setup
#3
hallamlab
closed
7 years ago
1
Move RNA nucleotide BLASTing to the grid
#2
hallamlab
closed
7 years ago
1
Slight Error in Pathway Tools input (ptools) in organism-params.dat file
#1
hallamlab
closed
11 years ago
1