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hammerlab
/
epidisco
Personalized cancer epitope discovery and peptide vaccine prediction pipeline
Apache License 2.0
30
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6
forks
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Display errors in `Input.t` parsing
#199
smondet
closed
6 years ago
0
Update documentation wrt wobidisco
#198
smondet
closed
7 years ago
0
Add the `tools/epirunner.sh` script
#197
smondet
closed
7 years ago
0
Update w.r.t. biokepi#478
#196
smondet
closed
7 years ago
0
with_topiary option not used, topiary run by default
#195
smondet
closed
7 years ago
0
README should link to specific tutorials
#194
iskandr
opened
7 years ago
0
Add a “run-locally” tutorial
#193
smondet
closed
7 years ago
2
Fix string formats to not mess with help pages (fixes #191)
#192
armish
closed
7 years ago
0
Weird cmdliner warning
#191
smondet
closed
7 years ago
0
Adding a quickstart-on-Secotrec doc
#190
julia326
closed
7 years ago
1
Fixes/changes for compatibility with Biokepi #468
#189
armish
closed
7 years ago
0
Add MHCflurry option to MHC predictor
#188
ihodes
opened
7 years ago
1
`name` is now a named argument to the `save` method
#187
armish
closed
7 years ago
3
Switch to `solvuu-build`
#186
smondet
closed
7 years ago
0
Submission helpers
#185
ihodes
closed
7 years ago
1
Parse out Input in the CLI
#184
ihodes
closed
7 years ago
1
Add NetMHC predictor
#183
ihodes
closed
7 years ago
0
Need quickstart guide for running on Secotrec
#182
julia326
opened
7 years ago
0
Add support for binding predictor configuration
#181
ihodes
closed
7 years ago
1
--results-path should verify in CLI that path is absolute
#180
ihodes
opened
7 years ago
0
Update README to point at Secotrec + get rid of disco.sh
#179
ihodes
opened
7 years ago
0
Add ppx_deriving_cmdliner as a dep
#178
ihodes
closed
7 years ago
1
Fix opam and improve travis
#177
smondet
closed
7 years ago
1
Missing dependency on ppx_deriving_cmdliner
#176
tavinathanson
closed
7 years ago
1
Broader memory option & use it for star mem limits
#175
ihodes
closed
7 years ago
2
STAR OOM
#174
ihodes
opened
7 years ago
1
Add instructions for running locally
#173
tavinathanson
closed
7 years ago
4
Small formatting fixes
#172
ihodes
closed
7 years ago
0
Switch CLI to Ppx_deriving_cmdliner
#171
ihodes
closed
7 years ago
2
Make epidisco workflows as compatible as possible across different dev versions
#170
armish
opened
7 years ago
0
Update docs/disco.sh to not use pipeline subcmd
#169
armish
closed
7 years ago
0
Reorder input BAMs by their reference
#168
ihodes
closed
7 years ago
0
Reorder input BAMs according to reference dict
#167
julia326
closed
7 years ago
1
disco.sh: Check whether configured and current IPs match when entering docker
#166
armish
closed
7 years ago
1
Force setup-epidisco overwrite the old biokepi_machine.ml
#165
armish
closed
7 years ago
1
Add CLI option to run kallisto on the RNA data
#164
armish
closed
7 years ago
1
Name with/without switches correctly
#163
ihodes
closed
7 years ago
0
Add switches for GATK steps
#162
ihodes
closed
7 years ago
1
Bring topiary back and run it by default
#161
armish
closed
7 years ago
3
Update to use new Biokepi API
#160
ihodes
closed
7 years ago
0
Add support for aggregating results from multiple pipeline runs
#159
armish
closed
7 years ago
1
Add topiary to the pipeline
#158
armish
closed
7 years ago
4
Vaxrank 4.0.0 runs fail when there is no vaccine available
#157
armish
closed
7 years ago
1
Update README link to ketrew+coclobas instructions
#156
ryan-williams
opened
7 years ago
0
Refactor & improve docs
#155
ihodes
closed
7 years ago
1
Note which arguments are required in the cmdliner docs
#154
ihodes
opened
7 years ago
0
disco.sh ketrew-ui uses old IP after new IP assigned
#153
tavinathanson
closed
7 years ago
1
Our FASTQ CLI-parsing can potentially lead to subtle errors
#152
ihodes
opened
7 years ago
0
Use /coclo instead of /tmp/coclo on the host to store disco files/logs
#151
armish
closed
7 years ago
3
Option to just call variants
#150
ihodes
closed
7 years ago
1
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