Permissions bugfix for guide design #7
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commit 63001da Author: NourHanafi <nour.hanafi@mail.utoronto.ca> Date: Fri Jul 22 18:33:00 2022 +0000 updated .gitignore commit d1070fc Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 23 13:24:44 2022 -0400 Delete sample.env commit 74c0ddd Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 22 16:51:30 2022 -0400 Fix README formatting commit d2c78b5 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 22 13:53:24 2022 -0400 Update README for current install setup commit 8189add Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 22 13:22:23 2022 -0400 yeet old setup scripts commit f57f5af Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Jun 13 14:00:27 2022 -0400 Add favicon to JBrowse commit 4c44647 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Jun 13 13:50:36 2022 -0400 Remove duplicate icon commit a0d9a0d Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Jun 13 13:31:08 2022 -0400 Bump JBrowse patch version commit 00a218c Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Jun 6 13:22:01 2022 -0400 Fix unnecessary +x outside of src/ commit 3d02099 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 17:52:35 2022 -0400 Disable Apache directory listing commit 7418d6d Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 17:23:01 2022 -0400 Replace JavaScript / redirect with proper server redirect commit e85c179 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 16:45:59 2022 -0400 Store JBrowse genome dropdown on bind mount commit 3ebed57 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 11:52:12 2022 -0400 Directly download UCSC Genome Browser kent binaries to /usr/local/bin commit d7c95d8 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 11:18:44 2022 -0400 Docker: mount tmpfs /run, /tmp commit 68e2b9d Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 11:17:43 2022 -0400 Fix Dicey module import paths as a result of Python 3 migration commit f6f0ab2 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Jun 3 11:17:02 2022 -0400 Fix missing names and permissions in new install process commit 358a088 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 2 17:53:56 2022 -0400 Fix not-updated Jinja error template path commit a30b411 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 2 17:53:31 2022 -0400 Fix some cursed regex buried in JSON string to find assembly name commit 6999d56 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 2 17:52:27 2022 -0400 Remove unused Python dependencies commit e05fd48 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 2 17:51:40 2022 -0400 Install Dicey to /usr/local/bin now that temporary directory is not needed commit 3ffe093 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Jun 2 17:14:10 2022 -0400 Fix Dicey, using Python 3, NamedTemporaryFile, new index paths commit 940bd59 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 1 17:49:37 2022 -0400 Fix Dicey index commit de47a89 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 1 17:17:09 2022 -0400 Slight cleanup create_segments commit 687e234 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 1 17:10:20 2022 -0400 Update paths for processed assemblies commit 950ee2a Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Jun 1 14:46:25 2022 -0400 New setup script that verifies assembly name, builds Dicey index, removes temporaries commit ed195e9 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Apr 6 15:21:27 2022 -0400 Improve download script to use checksum file for finding files Does not work with GRCm38 regulatory build due to checksum file inconsistencies commit 095e600 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Apr 6 14:59:18 2022 -0400 Initial draft of new standalone download script commit 9bbbad9 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 18:03:00 2022 -0400 Remove unused contents of bin/ that were also uncited Sources: UCSC, CRISPOR, possibly others - https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ - https://github.com/ucscGenomeBrowser/kent - https://github.com/maximilianh/crisporWebsite/tree/master/bin - https://github.com/maximilianh/maxtools commit 7e21763 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 17:31:24 2022 -0400 Remove licence until we get correct licensing details and attributions commit 835263e Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 17:29:00 2022 -0400 Remove vendored JBrowse commit 04f6477 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 15:38:59 2022 -0400 Cite background image commit c3e711a Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 15:30:43 2022 -0400 Clean up landing page cruft code and fix titles commit b24380f Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 15:16:17 2022 -0400 Cite the favicon commit 888430e Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 14:50:18 2022 -0400 Switch JBrowse data directories to be under data/ and create Docker mount Increase Ensembl REST API timeout commit 86ba295 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Mar 21 13:15:28 2022 -0400 Fix up Dicey install script commit 56e3a88 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 15:50:40 2021 -0500 Remove old install script commit 1ca839a Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 15:35:19 2021 -0500 Fix Dicey installation commit 99f1e22 Merge: aa1aed8 c7da06b Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 11:41:42 2021 -0500 Merge remote-tracking branch 'origin/master' into kevinlul/reproducibility commit aa1aed8 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 11:40:54 2021 -0500 Add paths.conf (to be removed) for image builds commit 49e57f7 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 11:39:10 2021 -0500 Remove dependency on outdated GitPython Only used to write commit hashes to MongoDB (but most are blank or ab62755) Current version if reinstalled has bug gitpython-developers/GitPython#983 without upgrading commit e008ff0 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 11:37:36 2021 -0500 Fix newly added genomes not being added to JBrowse.conf correctly commit 78171dc Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 11:36:56 2021 -0500 Write new Dockerfile, using apt and prebuilt binaries where possible commit ba8bd76 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed Dec 15 10:55:55 2021 -0500 Redownload some UCSC Genome Browser binaries to fix dynamic linking issues Source: https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/ Fixes missing libpng12.so problem that was hacked around commit c7da06b Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Dec 3 18:47:33 2021 +0000 Fix mysterious hardcoded genome in manual primer entry Parse querystring natively commit 7505d24 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Dec 3 18:24:33 2021 +0000 Fix outdated script and stylesheet references in manual primer entry commit 7d728a2 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Nov 22 14:15:27 2021 -0500 Ongoing work to restore reproducible builds Missing JBrowse, Primer3, BLAST, Dicey installs commit 012edd8 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Fri Oct 8 18:23:00 2021 +0000 Add helper scripts used for moving guides and primers between assemblies commit 777dca7 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed May 26 17:51:39 2021 +0000 Fix hardcoded gene assembly name in APEs commit 7952bf7 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Wed May 26 17:46:10 2021 +0000 Fix FetchAPE for changed directory structure, support all genomes commit 6dc68d1 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Mon Apr 26 16:26:58 2021 -0400 Replace contact links commit 96d49d2 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Mar 18 21:41:15 2021 +0000 Add genome assembly name to splash dropdown Disambiguates between assemblies for the same species commit dc25970 Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Thu Mar 18 21:35:23 2021 +0000 Fix bootstrap path for frontend, missing import in setup commit f47a093 Author: Hillary Elrick <47190916+helrick@users.noreply.github.com> Date: Wed Mar 17 14:30:45 2021 +0000 Permissions bugfix for guide design (#7) * ensuring permissions for web access are set * slightly more helpful error message (fixes issue with tmp.fa not being written) commit 1180e97 Author: Hillary Elrick <47190916+helrick@users.noreply.github.com> Date: Tue Mar 16 21:31:18 2021 +0000 Contents link typo + reorder README commit 2f43f8b Author: Kevin Lu <6320810+kevinlul@users.noreply.github.com> Date: Tue Mar 16 15:46:35 2021 -0400 Update README.md
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@kevinlul this shouldn't break anything on non-docker versions but wanted to make sure before merging
(fixes issue with tmp.fa not being written)