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Author Commit Message Labels Comments Date
peterjc
Basic BLAST XML merge implementation
Branches
split_blast
peterjc
Explicit failure for merging XML files
Branches
split_blast
peterjc
Merged stdout/stderr was missing newline between tasks
Branches
split_blast
peterjc
BLAST wrappers: Split FASTA query into parts
Branches
split_blast
peterjc
Size based FASTA splitting
Branches
split_blast
peterjc
Use FASTA splitting in BLAST wrappers
Branches
split_blast
peterjc
Simple FASTA splitting (no JSON metadata files)
Branches
split_blast
peterjc
Not all datatype splitters write a JSON file
Branches
split_blast
peterjc
Move FASTQ splitting from Sequence class to Fastq class
Branches
split_blast
peterjc
Enable splitting BLAST jobs up (doesn't work yet)
Branches
split_blast
jeremy goecks
Pack trackster scripts.
jeremy goecks
Trackster: save and restore tool state.
jeremy goecks
Better error message when bias correction/sequence data cannot be used in Cufflinks/compare/merge/diff.
Greg Von Kuster
Encode application name and link name when sending as request params to display application.
jeremy goecks
Trackster: for flexibility, use dictionaries in all object constructors. Fixed bugs associated with saving/restoring visualizations.
Greg Von Kuster
Do not allow conflicting datatypes included in a tool shed repository currently being installed to override datattypes already in the datatypes registry. Also, a bit of cleanup in handling datatypes included in repositories being activated / installed / deactivated / uninstalled. A bit more cleanup is still necessary.
Greg Von Kuster
Fixes for handling proprietary datatypes included in installed tool shed repositories - import proprietary class modules within the registry.
Nate Coraor
merge
Nate Coraor
closed branch dynamic_options_memory_fix
Branches
dynamic_options_memory_fix
Jeremy Goecks
Merged in jmchilton/umn-galaxy-central/dynamic_options_memory_fix (pull request #36)
John Chilton
One more fixed typo.
Branches
dynamic_options_memory_fix
John Chilton
Fix a typo made with last commit.
Branches
dynamic_options_memory_fix
John Chilton
Patch dynamic_options.py to just read just the first megabyte of an input dataset (if it is larger than that). Otherwise Galaxy will attempt the read the entire file into memory, this can causes crashes and freezeups without the user even selecting a bad input (for instance, if a large FASTQ file is the top most history item and a txt input is sought, Galaxy will freezeup as soon as the tool is clicked because it will try to load the options for the top item immediately by default). Though the implementation is not as clean, I am restricting it to a megabyte instead of a number of lines/options in case the top most history item has no line breaks. I imagine in that case the same problem could occur even if the input is restricted to a reasonable number of lines (say 100).
Branches
dynamic_options_memory_fix
jeremy goecks
Trackster: save and restore group/multi-track filters.
jeremy goecks
Merge
jeremy goecks
Trackster: filter bug fix and abstract filter display control.
jeremy goecks
Tophat wrapper modifications: (a) remove parameter junctions_filter and (b) change default value of max_multihits to 20.
Ross Lazarus
Updates to FastQC wrapper 1) improvement suggested by bwlang to pass the history file name in as the file name to fastqc so it appears in the outputs instead of the previously unhelpful internal galaxy filename 2) lack of html output from fastqc or return of non-zero error code now triggers job failure - outputs may still be there but at least it goes red.
jeremy goecks
Trackster: save and restore single track filters.
Nate Coraor
Make set_user_disk_usage.py object store-aware.
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