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Add NGSPlotDB-hg19-data recipe #9157

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Jun 11, 2018
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f0180d7
Add NGSPlotDB-hg19-data recipe
Jun 5, 2018
f4d66f2
Okay, lets test this
Jun 5, 2018
1975340
Add fix for ngsplot recipe
Jun 6, 2018
e9bd34b
Removed
Jun 6, 2018
3d214fb
Added @mbargull 's suggestions
Jun 6, 2018
e486e49
More suggestions
Jun 6, 2018
f5af8a9
Add suggestions of @mbargull
Jun 6, 2018
3ead683
Adjusted build.sh script
Jun 6, 2018
b1ae475
Removed source, as this is provided by post-link
Jun 6, 2018
cf50794
Hopefully more permant file URL
Jun 6, 2018
ae6e95a
Double check
Jun 6, 2018
1590814
Add check for hg19 database, removed sha256
Jun 6, 2018
e4eb39e
Better tests for ngsplot
Jun 6, 2018
721e3a2
More specific copying
Jun 6, 2018
054a918
Post and Pre Unlink scripts for r-ngsplot-hg19 updated
Jun 6, 2018
a76b668
No need for images in there
Jun 6, 2018
2a7f5e4
Fixing tests
Jun 6, 2018
484b1f2
Fixing tests
Jun 6, 2018
e16b597
Updated Build Script
Jun 6, 2018
95efbc3
Add Activate / Deactivate scripts for ENV variable
Jun 8, 2018
9c44497
Wrong path
Jun 8, 2018
b35f91a
Removing unrequired fbname
Jun 8, 2018
05101fa
Add exact name of package
Jun 8, 2018
8fb135d
Fixing pipes
Jun 8, 2018
30d2a97
Get rid of old activate script
Jun 8, 2018
9b168e6
Add patch for environment variable in R script
Jun 8, 2018
7977757
r-ngsplot: patch all scripts, avoid activation script
mbargull Jun 9, 2018
a40cf32
r-ngsplot: debugging: show output if test failed
mbargull Jun 9, 2018
f097068
r-ngsplot: try || in subshells
mbargull Jun 9, 2018
de5d1a6
r-ngsplot: add missing python dependency
mbargull Jun 9, 2018
88af4ed
r-ngsplot-hg19: fix variable name in post-link.sh
mbargull Jun 9, 2018
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2 changes: 1 addition & 1 deletion recipes/r-ngsplot-hg19/meta.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -19,4 +19,4 @@ test:
about:
home: 'https://github.com/shenlab-sinai/ngsplot'
license: GPL-2.0
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I wonder: does the database have another home URL? Is the database itself also licensed under the GPL-2.0?

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No, they are on GDrive and linked from the same Github repository - so I think its fine to use the same licence (as they didn't state explicitly another one).

Thanks for all the help - learned a lot here and will add two more databases today to finalize things here :-)

summary: 'Quick mining and visualization of NGS data by integrating genomic databases'
summary: 'HG19 genome database for NGSplot'
2 changes: 1 addition & 1 deletion recipes/r-ngsplot-hg19/post-link.sh
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
#!/bin/bash
FN="ngsplotdb_hg19_75_3.00.tar.gz"
URLS=(
"https://doc-0g-a0-docs.googleusercontent.com/docs/securesc/ha0ro937gcuc7l7deffksulhg5h7mbp1/jiksn2m41cm3dbspq0nqt102h6m6eo1o/1528221600000/01382619737792242945/*/0B5hDZ2BucCI6SURYWW5XdUxnbW8?e=download"
"https://drive.google.com/uc?export=download&id=0B5hDZ2BucCI6SURYWW5XdUxnbW8"
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👍 looks much saner 😄. galaxyproject/cargo-port#148 is probably still preferred, I think, but if that isn't merged in a timely manner, we can always package a new build for r-ngsplot-hg19 updating that URL later.

)
sha256="a3ad6daceec383f88faf3d3ee899f2bef37b3be2658ee9afa01e86404c0c92bd"
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MD5='172a6a93de3d1ae8a3ad6d6d79e911f7'

instead of sha256


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