Revision - c7d8cf6 - Look up the chain files instead of using hardcoded paths. - origin: https://github.com/genome/genome

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23 March 2024, 19:04:16 UTC

Revision c7d8cf68d263c3510dfc8162020ac9b4eceef12c authored by Thomas B. Mooney on 31 October 2018, 13:58:14 UTC, committed by Thomas B. Mooney on 31 October 2018, 13:58:14 UTC

Look up the chain files instead of using hardcoded paths.

I could imagine expanding this system to support many other chain files
we have, but for now this at least works right.  (I could also see
removing the shortcuts and always requiring a chain file, too... how
often do we need to convert to hg18 these days?)

1 parent ce7cecb

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Tip revision: c7d8cf68d263c3510dfc8162020ac9b4eceef12c authored by Thomas B. Mooney on 31 October 2018, 13:58:14 UTC
Look up the chain files instead of using hardcoded paths.

Tip revision: c7d8cf6

File	Mode	Size
alignment_summary @ 8932081
bam-readcount @ c044123
bam-window @ 572bfaf
bassovac @ 41b7bc4
bin
bmm @ 311e4d9
breakdancer @ 8f07f3d
configuration-manager @ f719544
copyCat @ 78b25a7
cron @ 584bc07
etc
fqgrep @ fe0206d
genome-db-cosmic @ bdec904
genome-db-omim @ d9b949a
genome-db-pfam @ e5acfb0
genome-env-tests
genome-music
genome-music-testdata @ 860ea75
genome-snapshot-deps @ 7d13e9e
genome-snapshot-testdata @ 72c0ded
genome-sys-user
genome-webserver
genome-www
getopt-complete @ 2dc69f2
gms-config @ 6ccaa62
gmt-sys-vmbuilder
graphite @ 705afc6
hooks
init
jenkins @ 80b7ba2
joinx @ e83e763
lib
pairoscope @ 5fdcd27
sciClone @ 723cadc
scripts
sff2fastq @ b815f97
somatic-sniper @ b83aab3
sqitch
tgi-etc @ 08ba1a6
tigra @ 6fe6b74
tigra-sv @ 715dda8
ur @ b63a182
varscan @ 83ae9d8
vendor
workflow @ c0f1230
.gitignore	-rw-r--r--	302 bytes
.gitmodules	-rw-r--r--	9.8 KB
.mailmap	-rw-r--r--	301 bytes
.test-tracker.conf	-rw-r--r--	353 bytes
LICENSE	-rw-r--r--	7.5 KB
README	-rw-r--r--	618 bytes
WHERE_TO_PUT_CODE	-rw-r--r--	2.4 KB
create-c-project.sh	-rwxr-xr-x	2.9 KB
create-project	-rwxr-xr-x	2.9 KB
test-data-relocate-me	l---------	55 bytes

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https://github.com/genome/genome

Look up the chain files instead of using hardcoded paths.

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