https://dev.arvados.org/https://dev.arvados.org/favicon.ico?15576888422010-05-08T15:59:40ZArvadosGET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20912010-05-08T15:59:40ZMadeleine Ballmpball@gmail.com
<ul></ul><p>For PGP9:</p>
<p>Aurora CO USA<br />female<br />cell line 21833<br />Incheon/PGP9<br /><a class="external" href="http://snp.med.harvard.edu/results/job/169">http://snp.med.harvard.edu/results/job/169</a></p>
<p>Can then hide (but use the photo): <a class="external" href="http://snp.med.harvard.edu/results/job/32">http://snp.med.harvard.edu/results/job/32</a></p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20922010-05-08T16:28:06ZTom Cleggtom@curii.com
<ul></ul><p>PGP9 now points to <a class="external" href="http://snp.med.harvard.edu/results/job/169/Rosalynn_Gill">http://snp.med.harvard.edu/results/job/169/Rosalynn_Gill</a></p>
<pre>
update jobs set human=16,label='cell line 21833, Incheon/PGP9',public=1 where id=169;
update jobs set public=0 where id=32;
</pre> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20932010-05-08T16:52:12ZTom Cleggtom@curii.com
<ul></ul><p>In evidence.oxf shell:</p>
<pre>
cd /home/get-evidence
cat public_html/config.php; mysqldump -ael -uevidence -p evidence >~/evidence-@date +%s@.sql
make update_genomes
</pre>
<p>In evidence.oxf mysql, remove links to previous data set (now that it is not listed as public on snp.med):</p>
<pre>
delete from variant_occurs where dataset_id='T/snp/32';
delete from datasets where dataset_id='T/snp/32';
</pre> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20942010-05-10T22:36:27ZMadeleine Ballmpball@gmail.com
<ul></ul><p>gff for Henry Louis Gates Jr (aka PGP12) can be found at:</p>
<p>wsa2@orchestra:/groups/pgp/illumina/pgp12$ md5sum HLGjr-snp.gff <br />7b7bbb5cfd4cd1433d1859b7b3c12c63 HLGjr-snp.gff</p>
<p>Please process in Trait-o-matic and upload to GET-Evidence. Phenotype should be available soon. Cell-line identifiers should also be available soon.</p>
<p>Henry Louis Gates Jr.<br />Cambridge, Ma<br />male<br />cell line<br />PGP12<br />Illumina</p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20952010-05-11T14:34:27ZMadeleine Ballmpball@gmail.com
<ul></ul><blockquote>
<p>wsa2@orchestra:/groups/pgp/illumina/pgp12$ md5sum HLGjr-snp.gff <br />7b7bbb5cfd4cd1433d1859b7b3c12c63 HLGjr-snp.gff</p>
</blockquote>
Abraham - uploaded it here:
<ul>
<li><a class="external" href="http://snp.med.harvard.edu/results/job/183">http://snp.med.harvard.edu/results/job/183</a></li>
</ul> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20962010-05-12T12:00:22ZTom Cleggtom@curii.com
<ul></ul><p>PGP12 now appears at <a class="external" href="http://snp.med.harvard.edu">http://snp.med.harvard.edu</a> -- currently with no portrait image.</p>
<p>Is it OK to use this image for his portrait?</p>
<p><a class="external" href="http://www.news.harvard.edu/gazette/2006/10.26/99-gates.html">http://www.news.harvard.edu/gazette/2006/10.26/99-gates.html</a></p>
<p><a class="external" href="http://www.law.washington.edu/News/Articles/Default.aspx?YR=2008&ID=henry_louis_gates">http://www.law.washington.edu/News/Articles/Default.aspx?YR=2008&ID=henry_louis_gates</a></p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20972010-05-12T12:19:24ZTom Cleggtom@curii.com
<ul></ul><p>PGP12 is now listed on evidence.personalgenomes.org as well.</p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20982010-05-17T15:05:45ZTom Cleggtom@curii.com
<ul></ul><p>Only remaining task is to choose a suitable image for PGP12.</p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=20992010-05-17T15:09:47ZMadeleine Ballmpball@gmail.com
<ul></ul><p>I think the CC-licensed Wikipedia image is fine for now:<br /><a class="external" href="http://en.wikipedia.org/wiki/Henry_Louis_Gates">http://en.wikipedia.org/wiki/Henry_Louis_Gates</a></p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=21002010-05-17T15:16:57ZTom Cleggtom@curii.com
<ul><li><strong>Resolution</strong> set to <i>fixed</i></li></ul><p>OK, wikipedia image is up.</p> GET-Evidence - Feature #487: Show full PGP9 and PGP12 genomes on snp.med and GET-Ehttps://dev.arvados.org/issues/487?journal_id=21512011-02-15T15:17:28ZWard Vandewegeward@curii.com
<ul><li><strong>Project</strong> changed from <i>19</i> to <i>GET-Evidence</i></li><li><strong>Category</strong> deleted (<del><i>GET-Evidence</i></del>)</li></ul>