hoffmangroup segway issues

hoffmangroup / segway

Application for semi-automated genomic annotation.

http://segway.hoffmanlab.org/

GNU General Public License v2.0

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issues

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Filenames in train.tab should all be relative to the train directory

#82 EricR86 opened 8 years ago
0
Different initial means (input.master) with minibatch and num-instances

#81 EricR86 closed 8 years ago
5
Segway should create observation files as a job submission instead of from the process submitting jobs.

#80 EricR86 opened 8 years ago
0
Improper specification of training directory (while identifying) results in nonsensical error message

#79 EricR86 opened 8 years ago
5
minibatch sorts windows by size, but then randomly selects from them

#78 EricR86 opened 8 years ago
2
GMTK jobs report "bad interpreter: Text file busy"

#77 EricR86 closed 7 years ago
15
Change `identify` to `annotate`

#76 EricR86 opened 8 years ago
2
GMTK does not allow last number of loadAccRange to be greater than 9999

#75 EricR86 opened 8 years ago
2
Segway readthedocs cuts off wide table columns in documentation

#74 EricR86 opened 8 years ago
0
segway does not delete job templates

#73 EricR86 closed 8 years ago
1
segway on SGE does not submit job arguments longer than 1024 chars

#72 EricR86 closed 8 years ago
7
Minibatch windows are not seeded

#71 EricR86 closed 8 years ago
3
Upon bundling, segway tries to reference an accumulator file for a run that was never queued in minibatch

#70 EricR86 closed 8 years ago
4
Segway does not detect overlapping regions in --include-coords/--exclude-coords bedfile

#69 EricR86 opened 8 years ago
1
Segway attempts to recover from last round run, rather than the one previous

#68 EricR86 opened 8 years ago
4
segway recovery (training mode) fails to copy over likelihood files

#67 EricR86 opened 8 years ago
3
new versions of bedToBigBed fail to convert layered BED files

#66 EricR86 closed 8 years ago
3
No active DRMAA session in segway

#65 EricR86 opened 8 years ago
5
Default track descriptions in are too long

#64 EricR86 opened 8 years ago
1
Segway should get the resolution used for training for identification

#63 EricR86 opened 8 years ago
4
Segway should put it's parent PID/Job ID in the job names it submits

#62 EricR86 opened 8 years ago
3
Setting resolution>1 fails for semi-supervised mode

#61 EricR86 closed 8 years ago
1
Segway process uses too much memory

#60 EricR86 closed 8 years ago
6
Warn when a track contains no zero values

#59 EricR86 opened 8 years ago
2
"How do I make segments longer?" FAQ page

#58 EricR86 closed 8 years ago
2
Default queue submitting along side specified queue from native specification (--cluster-opt)

#57 EricR86 opened 8 years ago
2
--split-sequences specifies number of GMTK frames and not number of base pairs

#56 EricR86 closed 8 years ago
2
Bug in exit_status from get_job_info_exit_status

#55 EricR86 closed 8 years ago
4
Tests assume undefined $TMPDIR to run correctly

#54 EricR86 closed 8 years ago
4
Segtable default minimum length doesn't adjust for changes in ruler

#53 EricR86 closed 8 years ago
1
Segway silently ignores DRMAA if installed incorrectly

#52 EricR86 closed 8 years ago
8
When setting a mem-usage smaller than 10MB, segway will fail to run regardless of input

#51 EricR86 closed 8 years ago
1
segway no longer output help

#50 EricR86 closed 9 years ago
3
A track can be specified that exists in more than one genomedata

#49 EricR86 closed 9 years ago
2
Posterior not supported with multiple genomedata archives

#48 EricR86 opened 9 years ago
0
Better handling when --ruler is set and no segment table is specified

#47 EricR86 closed 9 years ago
2
`--enforce-coords` results in ERROR: RV 'frameIndex...' has cardinality ..., but current frame value ... too large to store in RV with this cardinality

#46 EricR86 closed 9 years ago
3
Better checks for valid genomedata archives

#45 EricR86 opened 9 years ago
1
Better default for --num-labels

#44 EricR86 closed 9 years ago
1
Allow manual weighting of different tracks

#43 EricR86 opened 9 years ago
0
Too many log files in single directory

#42 EricR86 opened 9 years ago
0
Local Segway should limit number of jobs to the actual amount of processors

#41 EricR86 opened 9 years ago
1
Default ruler should be 10x resolution if a seg table is not specified

#40 EricR86 closed 9 years ago
1
"pip install segway" doesn't work without installing other python packages manually

#39 EricR86 closed 8 years ago
1
Soft labeling for Semi-supervised mode

#38 EricR86 closed 9 years ago
7
Semisupervised Mean Generate from Track data in supervision region.

#37 EricR86 opened 9 years ago
3
Retrive Observation from the Recovery Directory in Recovery Mode

#36 EricR86 opened 9 years ago
3
track spec name checking

#35 EricR86 opened 9 years ago
2
Explicitly limit the number of current running segway jobs.

#34 EricR86 opened 9 years ago
4
Change GMTK output from text to HDF5 format

#33 EricR86 opened 9 years ago
0

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