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All the flask applications mentioned above make use of python-requests
library which needs the CA certificate bundle present within the
environment that each application runs in. The nss-certs package
installs the appropriate CA certificate bundles.
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Set up basic database settings to ensure persistence of data across
restarts.
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* .guix-channel: Upgrade guix channel to 2394a7f.
* gn/packages/bioinformatics.scm (pplacer)[inputs]: Replace gsl-static
with (gsl "static").
* gn/packages/ocaml.scm (ocaml4.07-gsl-1)[inputs]: Replace gsl-static
with (gsl "static").
* gn/packages/static.scm (wfmash-static)[inputs]: Replace gsl-static
with (gsl "static").
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* gn/packages/bioinformatics.scm (pplacer): Use G-expressions.
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* gn/packages/ocaml.scm (ocaml4.07-gsl-1): Use G-expressions.
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* gn/packages/bioinformatics.scm (graphaligner): Update to 1.0.19.
[native-inputs]: Add (jemalloc "bin").
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* gn/packages/bioinformatics.scm (graphaligner): Use G-expressions.
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* gn/packages/bioinformatics.scm (smoothxg): Update to 0.8.0.
[arguments]: Remove architecture-specific -march=armv8-a+simd flag.
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* gn/packages/bioinformatics.scm (odgi): Update to 0.9.0.
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* gn/packages/bioinformatics.scm (seqwish): Update to 0.7.11.
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Pull in fixes for WGCNA and CTL analyses.
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Pull in Pair-Scan output paths fixes
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Include R scripts in installed files.
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Pull in changes fixing paths for rqtl_wrapper.R script.
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* Add missing python package.
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Update to latest commit with @pjotr's changes.
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Push fix below:
https://github.com/genenetwork/genenetwork2/commit/8618fdc8f4c05153f48e1afdbf9d2c337ba79929
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This pushes fix for the bug caused by using relative paths for font
files.
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This update pushes some logging of a font file. The purpose is to
debug relative paths, and prove/disprove a hypothesis.
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This reverts commit 7eaa7028ffe3e8b0d5dfe242da87dd76930f637e.
This does not include all the dependencies needed to run GEMMA. These
were included with commit ab2ae88f2698cde22cae05c432f0f1ae0db7b070
later, but that also had to be reverted due to another issue altogether.
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This reverts commit ab2ae88f2698cde22cae05c432f0f1ae0db7b070.
At this point, running GEMMA will fail because it attempts to extract
files into the /tmp directory, which leads to permission issues when
there is an attempt to change the permission bits of /tmp.
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This reverts commit 57444f7e0f360eb88e11aed4217143cafb164325.
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This reverts commit 4addf0abad6c05b060ea4947512c6b413e3b750b.
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* gn/packages/genenetwork.scm: (genenetwork2) [propagated-inputs]: Add
javascript-ace, javascript-diff, javascript-diff2html,
javascript-diff2html-ui javascript-highlight, javascript-highlight-ui,
javascript-marked, javascript-marked-highlight.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm (javascript-highight-ui): New package.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm (javascript-highlight): New package.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm (javascript-diff): New package.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm (javascript-diff2html-ui): New package.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm (javascript-diff2html): New package.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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* gn/packages/javascript.scm: (javascript-ace): Update License. Apply
guix style.
Reviewed-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
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Update the hash to pull in fixes for the following ops issues:
* Installing of Jinja2 text-file templates for emails
* Logging out unhandled exceptions as errors for easier debugging
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