George Hartzell hartzell
hartzell
/ spack-build.out
Created
November 29, 2016 21:12
shiny-server spack-build.out w/ '-- Installing' lines filtered out.
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| ==> 'cmake' '/rss/spack-20161101/var/spack/stage/shiny-server-2016-11-04-iwyadliuj7yuyoxpu5dlgneaxq3ydlkv/shiny-server' '-DCMAKE_INSTALL_PREFIX:PATH=/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/shiny-server-2016-11-04-iwyadliuj7yuyoxpu5dlgneaxq3ydlkv' '-DCMAKE_BUILD_TYPE:STRING=RelWithDebInfo' '-DCMAKE_VERBOSE_MAKEFILE:BOOL=ON' '-DCMAKE_INSTALL_RPATH_USE_LINK_PATH:BOOL=FALSE' '-DCMAKE_INSTALL_RPATH:STRING=/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/shiny-server-2016-11-04-iwyadliuj7yuyoxpu5dlgneaxq3ydlkv/lib:/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/shiny-server-2016-11-04-iwyadliuj7yuyoxpu5dlgneaxq3ydlkv/lib64:/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/bzip2-1.0.6-iro5tie325lhmx2ph36nox3namcf4wqm/lib:/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/cairo-1.14.0-crpytuydkcgzatow3xfst5cc5episr5e/lib:/rss/spack-20161101/opt/spack/linux-centos7-x86_64/gcc-5.4.0/fontconfig-2.11.1-ti2zz3wpp4yflrik6p7pt5nih7ngdhip/lib:/rss/spack-20161 |
hartzell
/ disable_cli_sshd.groovy
Created
November 10, 2016 16:15
A groovy script to disable the built-in sshd server in Jenkins
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| // Drop this into init.groovy.d so that it gets executed at startup time. | |
| // One could also use this script to explicitly set a port. | |
| def inst = Jenkins.getInstance() | |
| def sshDesc = inst.getDescriptor("org.jenkinsci.main.modules.sshd.SSHD") | |
| sshDesc.setPort(-1) | |
| sshDesc.getActualPort() | |
| sshDesc.save() |
hartzell
/ gist:dc5e258b27d7c976f194
Created
March 28, 2015 22:20
Fixes to mousex-getopt tests to handle underlying changes to getopt-long-descriptive.
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| allons:tmp georgewh$ diff -u -r mousex-getopt-0.35 mousex-getopt-0.35.BORKED | |
| Only in mousex-getopt-0.35: Build | |
| Only in mousex-getopt-0.35: MYMETA.json | |
| Only in mousex-getopt-0.35: MYMETA.yml | |
| Only in mousex-getopt-0.35: _build | |
| Only in mousex-getopt-0.35: blib | |
| diff -u -r mousex-getopt-0.35/t/104_override_usage.t mousex-getopt-0.35.BORKED/t/104_override_usage.t | |
| --- mousex-getopt-0.35/t/104_override_usage.t 2015-03-28 15:13:44.000000000 -0700 | |
| +++ mousex-getopt-0.35.BORKED/t/104_override_usage.t 2014-03-10 00:02:07.000000000 -0700 | |
| @@ -44,8 +44,8 @@ |
hartzell
/ feature-dump-2.sql
Last active
August 29, 2015 14:05
Dump the features related to a hard-coded starting feature, using two common table expressions (one recursive to build the set, one not recursive to expand set of columns)
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| -- Here's an example that takes the output of the recursive CTE | |
| -- and then decorates it with details about the features and relationships. | |
| with recursive pair(initial_feature, | |
| subj_feature_id, relationship_id, obj_feature_id, | |
| feat_id_path, | |
| cycle | |
| ) as | |
| ( | |
| select subj.feature_id, | |
| subj.feature_id, fr.feature_relationship_id, obj.feature_id, |
hartzell
/ feature-dump-1.sql
Last active
August 29, 2015 14:05
Dump all of the features related to a starting feature (hardcoded....) using a recursive common table expression.
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| -- This works, starts with a feature and lists all of the features | |
| -- it's related to, deals with cycles, homology seems to be reflexive | |
| -- and symmetric. | |
| with recursive | |
| -- info about a subject/object pair | |
| pair(initial_feature, | |
| subj_feature_id, subj_name, subj_uniquename, subjterm_name, | |
| relterm_name, | |
| obj_feature_id, obj_name, obj_uniquename, objterm_name, | |
| feat_id_path, |
hartzell
/ exons-and-their-mrnas.sql
Last active
August 29, 2015 14:05
Build a table of exons that belong to more than one mRNA (exon name, {list of mRNA names}). Written as an excuse to play with common table expressions.
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| -- An exercise in Common Table Expessions. There are probably | |
| -- faster solutions.... | |
| -- Run this against Flybase and discover the exons that belong | |
| -- to more than one transcripts. | |
| -- exon_name | transcripts | |
| -- 14-3-3epsilon:1 | {14-3-3epsilon-RB,14-3-3epsilon-RD} | |
| -- 14-3-3epsilon:2 | {14-3-3epsilon-RA,14-3-3epsilon-RC} | |
| -- 14-3-3epsilon:3 | {14-3-3epsilon-RA,14-3-3epsilon-RB,14-3-3... | |
| with | |
| -- collect a bit of cvterm info |
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