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dib-lab
/
elvers
(formerly eelpond) an automated RNA-Seq workflow system
https://dib-lab.github.io/elvers/
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'basename' may not be properly quoted
#63
ctb
opened
5 years ago
2
Add eel icon to documentation
#62
charlesreid1
closed
5 years ago
0
put nice workflow diagram into the documentation
#61
ctb
opened
5 years ago
0
add a slower quickstart with configuration?
#60
ctb
opened
5 years ago
2
allow workflow to be specified in the configfile
#59
ctb
closed
5 years ago
0
make 'salmon' or 'quantify' an equal citizen
#58
ctb
opened
5 years ago
1
Jetstream image?
#57
johnsolk
opened
5 years ago
2
one possible approach to testing: inspect command lines
#56
ctb
opened
5 years ago
1
document and test --extra_config
#55
ctb
opened
5 years ago
2
terminology idea?
#54
ctb
opened
5 years ago
1
PEAR failing on travis
#53
bluegenes
closed
5 years ago
0
support the execution of a bunch of notebooks upon completion
#52
ctb
opened
5 years ago
2
fix link to eel_pond_workflow in about_and_configure doc
#51
bluegenes
closed
5 years ago
0
pass unlock into snakemake
#50
bluegenes
closed
5 years ago
0
maybe we should be retrying downloads on travisci?
#49
ctb
closed
5 years ago
1
[MRG] fix pear benchmark; add plass to travis
#48
bluegenes
closed
5 years ago
1
[WIP] another try at keeping the cache unchanged
#47
ctb
closed
5 years ago
1
[DO NOT MERGE] a branch for @ctb's GGG 201b course, Winter 2019, UC Davis.
#46
ctb
closed
5 years ago
0
check replicates for diffexp analysis
#45
bluegenes
opened
5 years ago
0
[MRG] rename (& simplify) example files
#44
ctb
closed
5 years ago
3
[MRG] print params to stdout
#43
bluegenes
closed
5 years ago
0
make editing configfile easier
#42
bluegenes
closed
5 years ago
0
make preparing samples.tsv easier
#41
ctb
opened
5 years ago
2
improve print_workflows option
#40
bluegenes
opened
5 years ago
2
osf downloads do not always work on travis ci
#39
ctb
closed
5 years ago
4
[WIP] fix travis caching of miniconda/
#38
ctb
closed
5 years ago
1
[MRG] enable extra configs
#37
bluegenes
closed
5 years ago
2
fix force options in run_eelpond
#36
bluegenes
opened
5 years ago
0
[MRG] default do not restart tools if they fail
#35
bluegenes
closed
5 years ago
0
[MRG] better alternative to specify the "full" workflow
#34
bluegenes
closed
5 years ago
2
update test data input assembly
#33
bluegenes
closed
5 years ago
0
[MRG] Write more docs
#32
bluegenes
closed
5 years ago
1
[MRG] back to macmanes params
#31
bluegenes
closed
5 years ago
0
`get_data` target assumes input data is gzipped.
#30
ctb
opened
5 years ago
3
[MRG] use 6 threads on travis
#29
ctb
closed
5 years ago
0
'quantify' target is currently failing.
#28
ctb
closed
5 years ago
5
[MRG] fix conda package caching
#27
ctb
closed
5 years ago
1
dammit should fail once and for all, rather than try repeatedly
#26
ctb
closed
5 years ago
2
how do you pass in custom param files?
#25
ctb
closed
5 years ago
2
[MRG] Adjust language in docs for trimmomatic a little bit
#24
ctb
closed
5 years ago
0
how specify alternative location for databases?
#23
ctb
opened
5 years ago
6
[MRG] fix assembly input
#22
bluegenes
closed
5 years ago
1
[MRG] add tool benchmarking
#21
bluegenes
closed
5 years ago
1
[MRG] move env file
#20
bluegenes
closed
5 years ago
0
remove large files from git commit history
#19
ctb
opened
5 years ago
1
maybe rename ep_utils/eelpond_environment.yaml?
#18
ctb
closed
5 years ago
1
submodule 'databases' fails when `-t 6` specified
#17
ctb
closed
5 years ago
5
resource usage!
#16
ctb
opened
5 years ago
4
citation printing
#15
bluegenes
opened
5 years ago
1
use 'conda activate' instead of 'source activate'?
#14
ctb
closed
5 years ago
1
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