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#bioconda

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Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version now is 1.6.0!</p><p>Give us some time, and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release, you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you discover any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a>.</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.6.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.6.0</span></a> for details. Here is the header of the changelog:</p><p>𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):<br>𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬</p><p>* added github action to label long pending issues as 'stale' (<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/239" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/239</span></a>) ([6d7c50a](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/6d7c50ae492c9557b6cc39119c572c5b5ef1b341" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/6d7c50ae492c9557b6cc39119c572c5b5ef1b341</span></a>))<br>* treat sbatch errors as job errors instead of workflow errors (<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/322" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/322</span></a>) ([5e38507](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/5e3850762c73abf1fff8ba9e1e8c18379251041f" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/5e3850762c73abf1fff8ba9e1e8c18379251041f</span></a>))<br>* using the current version of the announcement bot for Mastodon (<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/333" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/333</span></a>) ([03e0e24](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/03e0e2426edbe2957be93f02f3ae3834f710faff" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/03e0e2426edbe2957be93f02f3ae3834f710faff</span></a>))</p><p>𝐁𝐮𝐠 𝐅𝐢𝐱𝐞𝐬</p><p>* allow unse...</p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version now is 1.5.0!</p><p>Give us some time, and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release, you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you discover any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a>.</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.5.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.5.0</span></a> for details. Here is the header of the changelog:</p><p>𝑅𝑒𝑙𝑒𝑎𝑠𝑒 𝑁𝑜𝑡𝑒𝑠 (𝑝𝑜𝑠𝑠𝑖𝑏𝑙𝑦 𝑎𝑏𝑏𝑟𝑖𝑔𝑒𝑑):<br>𝐅𝐞𝐚𝐭𝐮𝐫𝐞𝐬</p><p>* measuring compute efficiency per job ([#221](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/221" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/221</span></a>)) ([3cef6b7](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/3cef6b7889c8ba09280f345bade3497b144bedc7" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/3cef6b7889c8ba09280f345bade3497b144bedc7</span></a>))</p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version now is 1.4.0!</p><p>Give us some time, and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release, you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you discover any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a>.</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.4.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.4.0</span></a> for details. Here is the header of the changelog:</p><p>Release Notes (possibly abbriged):<br>### Features</p><p>* adding reservation flag ([#323](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/323" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/323</span></a>)) ([d4e0a0f](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/d4e0a0f4160f5336c5bf36be8f097b8a01f77718" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/d4e0a0f4160f5336c5bf36be8f097b8a01f77718</span></a>))</p><p>### Documentation</p><p>* review and edit new docs ([#237](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues/237" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues/237</span></a>)) ([ec82a70](<a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/commit/ec82a70b95652afcbc21d44a4dbca14d78dc8936" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/commit/ec82a70b95652afcbc21d44a4dbca14d78dc8936</span></a>))</p>
Bjoern Gruening<p>Benchmarking and rebuilding bwa-mem2 with LLVM vs. GCC.</p><p><a href="https://github.com/bioconda/bioconda-recipes/pull/56242" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">github.com/bioconda/bioconda-r</span><span class="invisible">ecipes/pull/56242</span></a></p><p><a href="https://fosstodon.org/tags/bioconda" class="mention hashtag" rel="tag">#<span>bioconda</span></a></p>
Felix Wiegand<p>Another major new <a href="https://mastodon.social/tags/alignoth" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>alignoth</span></a> release is now available on <a href="https://mastodon.social/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a> ⭐ Our read alignment plots now include a coverage plot on top as well as improved visualization of overlapping read pairs! Check out our interactive demo at <a href="https://alignoth.github.io/preview.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">alignoth.github.io/preview.html</span><span class="invisible"></span></a></p><p><span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version now is 1.3.6!</p><p>Give us some time, and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release, you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you discover any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a>.</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.3.6" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.3.6</span></a> for details. Here is the header of the changelog:</p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version is 1.2.17!</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.2.17" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.2.17</span></a> for details.</p><p>Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and @johanneskoester</p><p>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a></p>
Peter Cock<p>There is quite a backlog of open pull requests for <a href="https://fediscience.org/tags/BioConda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>BioConda</span></a>, with a lot of new recipes judging from the little bit of triage I just did <a href="https://github.com/bioconda/bioconda-recipes/pulls" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/bioconda/bioconda-r</span><span class="invisible">ecipes/pulls</span></a></p>
Christian Meesters<p>Due to maintenance of the cluster I usually work on, only minor updates to the <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> plugin for <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> compatible workflows could be made.</p><p>However, it now has better GPU support by generic resources. Already on <a href="https://fediscience.org/tags/PyPi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>PyPi</span></a>, soon on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a>, too.</p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version is '1.0.0'!</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v1.0.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v1.0.0</span></a> for details.</p><p>Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a></p><p><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleComputing</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version is '0.15.1'!</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.1" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v0.15.1</span></a> for details.</p><p>Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a></p><p><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleComputing</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
Phil Ewels<p>By default, the <a href="https://genomic.social/tags/Seqera" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Seqera</span></a> <a href="https://genomic.social/tags/Containers" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Containers</span></a> web interface searches the <a href="https://genomic.social/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a> and <a href="https://genomic.social/tags/condaforge" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>condaforge</span></a> channels 📦</p><p>But did you know that you can prepend your search with *any* conda channel?</p><p>Try it out: <a href="https://seqera.io/containers/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="">seqera.io/containers/</span><span class="invisible"></span></a></p>
Snakemake Release Robot<p>Beep, Beep - I am your friendly <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> release announcement bot.</p><p>There is a new release of the Snakemake executor for <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> systems. Its version is '0.15.0'!</p><p>See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.15.0" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v0.15.0</span></a> for details.</p><p>Give us some time and you will automatically find the plugin on <a href="https://fediscience.org/tags/Bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Bioconda</span></a> and <a href="https://fediscience.org/tags/Pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Pypi</span></a>.</p><p>If you want to discuss the release you will find the maintainers here on Mastodon!<br><span class="h-card" translate="no"><a href="https://fediscience.org/@rupdecat" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>rupdecat</span></a></span> and <span class="h-card" translate="no"><a href="https://fosstodon.org/@johanneskoester" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>johanneskoester</span></a></span></p><p>If you find any issues, please report them on <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/issues" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/issues</span></a></p><p><a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> <a href="https://fediscience.org/tags/ReproducibleComputing" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleComputing</span></a> <a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
Bjoern Gruening<p><a href="https://fosstodon.org/tags/bioconda" class="mention hashtag" rel="tag">#<span>bioconda</span></a> has reached 11.111 packages. Great end of the year 2024. Thanks a lot for all contributors and the Bioconda Core team to keep the infrastructure up and running.</p>
Christian Meesters<p>New release for the <a href="https://fediscience.org/tags/Snakemake" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>Snakemake</span></a> <a href="https://fediscience.org/tags/SLURM" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>SLURM</span></a> plugin to use on <a href="https://fediscience.org/tags/HPC" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>HPC</span></a> clusters.</p><p>A bug fix release to reliably submit and cancel jobs, where admins overwrote `sbatch` behaviour with additional output on `stderr`. See <a href="https://github.com/snakemake/snakemake-executor-plugin-slurm/releases/tag/v0.11.2" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">github.com/snakemake/snakemake</span><span class="invisible">-executor-plugin-slurm/releases/tag/v0.11.2</span></a> (will automatically be released on <a href="https://fediscience.org/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a> and <a href="https://fediscience.org/tags/pypi" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>pypi</span></a>)</p><p>Finally resuming work on the plugin. It has been a stressful time, lately.</p><p><a href="https://fediscience.org/tags/ReproducibleResearch" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>ReproducibleResearch</span></a> <a href="https://fediscience.org/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://fediscience.org/tags/OpenScience" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>OpenScience</span></a></p>
James Fellows Yates<p>And if anyone from <a href="https://genomic.social/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a> sees this and likes it, I would be happy to chat about maybe porting it to proper docs if of interest :)</p><p>[🧵 2/2]</p>
James Fellows Yates<p>Do you work in <a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a>, love <a href="https://genomic.social/tags/conda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>conda</span></a> &amp; <a href="https://genomic.social/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a>, but didn't know how to start adding (or debugging) your/someone else's software to it?</p><p>Here's a three-part (opinionated) guide for the <a href="https://genomic.social/tags/microbifinie" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microbifinie</span></a> blog on just that, based on my own experiences!</p><p>Adding: <a href="https://ubinfie.github.io/2024/08/16/adding-to-bioconda-quickguide.html" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">ubinfie.github.io/2024/08/16/a</span><span class="invisible">dding-to-bioconda-quickguide.html</span></a><br>Updating: <a href="https://ubinfie.github.io/2024/08/16/updating-bioconda-recipe-quickguide" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">ubinfie.github.io/2024/08/16/u</span><span class="invisible">pdating-bioconda-recipe-quickguide</span></a><br>Debugging: <a href="https://ubinfie.github.io/2024/08/16/debugging-bioconda-build-quickguide" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">ubinfie.github.io/2024/08/16/d</span><span class="invisible">ebugging-bioconda-build-quickguide</span></a></p><p>Many thanks to George Bouras for nudging me to formalise my notes, and <span class="h-card" translate="no"><a href="https://genomic.social/@shl" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>shl</span></a></span> , Wytamma Wirth, and <span class="h-card" translate="no"><a href="https://mstdn.science/@pmenzel" class="u-url mention" rel="nofollow noopener" target="_blank">@<span>pmenzel</span></a></span> for the testing/review!</p><p>[🧵1/2]</p>
conda<p>Lately, we’ve seen some concern and confusion among our users, so we want to clear things up. In this blog post, we’re breaking down the <a href="https://fosstodon.org/tags/conda" class="mention hashtag" rel="tag">#<span>conda</span></a> ecosystem: the tools, the channels (like <a href="https://fosstodon.org/tags/conda" class="mention hashtag" rel="tag">#<span>conda</span></a>-forge, <a href="https://fosstodon.org/tags/bioconda" class="mention hashtag" rel="tag">#<span>bioconda</span></a>), how to get started, and how multi-stakeholder governance ensures the ecosystem remains reliable and accessible for everyone. 👉 <a href="https://conda.org/blog/2024-08-14-conda-ecosystem-explained" target="_blank" rel="nofollow noopener" translate="no"><span class="invisible">https://</span><span class="ellipsis">conda.org/blog/2024-08-14-cond</span><span class="invisible">a-ecosystem-explained</span></a><br />This was a collaborative effort from across conda ecosystem, and we hope it’s helpful for the whole community. 🤗</p>
Bjoern Gruening<p><a href="https://fosstodon.org/tags/bioconda" class="mention hashtag" rel="tag">#<span>bioconda</span></a> <a href="https://fosstodon.org/tags/usegalaxy" class="mention hashtag" rel="tag">#<span>usegalaxy</span></a> <span class="h-card" translate="no"><a href="https://mstdn.science/@elixir_europe" class="u-url mention">@<span>elixir_europe</span></a></span> all my favourites in one slide :-)<br />59 new tools in Galaxy for Exposome research!</p>
Genomicalist 🧬🦠🧫👩‍💻<p>CompareM2 is published on Bioconda! Enjoy!</p><p>For all of your prokaryotic genomes-to-report needs.</p><p><a href="https://comparem2.readthedocs.io/en/latest/" rel="nofollow noopener" translate="no" target="_blank"><span class="invisible">https://</span><span class="ellipsis">comparem2.readthedocs.io/en/la</span><span class="invisible">test/</span></a></p><p><a href="https://genomic.social/tags/bioinformatics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioinformatics</span></a> <a href="https://genomic.social/tags/genomics" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>genomics</span></a> <a href="https://genomic.social/tags/microbiology" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>microbiology</span></a> <a href="https://genomic.social/tags/bioconda" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>bioconda</span></a> <a href="https://genomic.social/tags/foss" class="mention hashtag" rel="nofollow noopener" target="_blank">#<span>foss</span></a></p>
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