[med-svn] [crossbow] 05/07: Update upstream source from tag 'upstream/1.2.0'
Andreas Tille
tille at debian.org
Sun Dec 3 18:02:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository crossbow.
commit b7d37ef20a52ea6dae5e93881d96e90671569f5f
Merge: 98ebe31 b74ffb2
Author: Andreas Tille <tille at debian.org>
Date: Sun Dec 3 18:57:15 2017 +0100
Update upstream source from tag 'upstream/1.2.0'
Update to upstream version '1.2.0'
with Debian dir da86b4e50c05b47de4a15853887f6b15742d8d80
AWS.pm | 66 +
Align.pl | 490 +++++
BinSort.pl | 301 +++
CBFinish.pl | 205 ++
CheckDirs.pl | 112 +
Copy.pl | 619 ++++++
Counters.pl | 157 ++
Counters.pm | 164 ++
CrossbowIface.pm | 1495 +++++++++++++
Get.pm | 499 +++++
LICENSES | 12 +
LICENSE_ARTISTIC | 114 +
LICENSE_GPL3 | 674 ++++++
MANUAL | 1708 +++++++++++++++
MANUAL.markdown | 2144 ++++++++++++++++++
Makefile | 167 ++
MapWrap.pl | 296 +++
NEWS | 225 ++
ReduceWrap.pl | 459 ++++
Soapsnp.pl | 396 ++++
TOOLNAME | 1 +
TUTORIAL | 1 +
Tools.pm | 523 +++++
Util.pm | 137 ++
VERSION | 1 +
Wrap.pm | 67 +
cb_emr | 136 ++
cb_hadoop | 214 ++
cb_local | 249 +++
contrib/ForkManager.pm | 412 ++++
contrib/Sort.pm | 1081 ++++++++++
doc/images/AWS_cb_e_coli_fillin.png | Bin 0 -> 135083 bytes
doc/images/AWS_cb_mouse17_fillin.png | Bin 0 -> 139496 bytes
doc/images/AWS_console.png | Bin 0 -> 186671 bytes
doc/images/AWS_console_debug.png | Bin 0 -> 159560 bytes
doc/images/AWS_console_upper_left.png | Bin 0 -> 94221 bytes
doc/images/AWS_create_new.png | Bin 0 -> 62026 bytes
doc/manual.html | 3832 +++++++++++++++++++++++++++++++++
doc/strip_markdown.pl | 39 +
doc/style.css | 145 ++
doc/website/faq.shtml | 34 +
doc/website/faq.ssi | 15 +
doc/website/foot.ssi | 9 +
doc/website/index.html | 9 +
doc/website/index.shtml | 68 +
doc/website/manual.shtml | 33 +
doc/website/manual.ssi | 3821 ++++++++++++++++++++++++++++++++
doc/website/news.shtml | 35 +
doc/website/old_news.ssi | 214 ++
doc/website/push.sh | 17 +
doc/website/recent_news.ssi | 150 ++
doc/website/rhsidebar.ssi | 126 ++
doc/website/top.ssi | 12 +
doc/website/tutorial.shtml | 234 ++
doc/website/ui.html | 9 +
emr/util/pull_push.sh | 36 +
emr/util/push.sh | 26 +
example/e_coli/full.manifest | 4 +
example/e_coli/small.manifest | 3 +
example/mouse17/full.manifest | 11 +
example/mouse17/small.manifest | 3 +
reftools/chimp_ensembl.sh | 63 +
reftools/db2ssnp | 314 +++
reftools/db2ssnp_ce4 | 30 +
reftools/db2ssnp_ce6 | 30 +
reftools/db2ssnp_hg19 | 61 +
reftools/db2ssnp_mm9 | 54 +
reftools/db2ssnp_mm9_chr17 | 30 +
reftools/e_coli_jar | 74 +
reftools/ensembl_snps.pl | 234 ++
reftools/fasta_cmap.pl | 70 +
reftools/fly_ensembl.sh | 67 +
reftools/hg19_jar | 79 +
reftools/human_ensembl.sh | 58 +
reftools/mm9_chr17_jar | 51 +
reftools/mm9_jar | 79 +
reftools/mouse_ensembl.sh | 58 +
reftools/sanity_check.pl | 59 +
reftools/shared.sh | 156 ++
reftools/yeast_ensembl.sh | 55 +
soapsnp/COPYING | 674 ++++++
soapsnp/binarize.cc | 71 +
soapsnp/call_genotype.cc | 584 +++++
soapsnp/chromosome.cc | 254 +++
soapsnp/main.cc | 460 ++++
soapsnp/makefile | 30 +
soapsnp/matrix.cc | 67 +
soapsnp/normal_dis.cc | 24 +
soapsnp/prior.cc | 111 +
soapsnp/rank_sum.cc | 128 ++
soapsnp/readme | 233 ++
soapsnp/release | 9 +
soapsnp/soap_snp.h | 793 +++++++
util/build_soapsnp.sh | 174 ++
util/package.bash | 79 +
webui/S3Util.pm | 118 +
webui/crossbow.pl | 977 +++++++++
webui/fill_e_coli_generic.sh | 37 +
webui/fill_mm9chr17_generic.sh | 38 +
webui/push.sh | 30 +
webui/push_test.sh | 33 +
webui/setup.sh | 20 +
webui/wait.gif | Bin 0 -> 4178 bytes
103 files changed, 28576 insertions(+)
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