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<h3>
Liubov Chuprikova pushed to branch master
at <a href="https://salsa.debian.org/med-team/ncbi-tools6">Debian Med / ncbi-tools6</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb">71bca8b8</a></strong>
<div>
<span>by Liubov Chuprikova</span>
<i>at 2018-03-28T19:34:58+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Autopkgtest. More tests, but will be more
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
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<li class="file-stats">
<a href="#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
debian/source/include-binaries
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<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<li class="file-stats">
<a href="#acfa977d03b7652c5322791224159451a90ea444">
<span class="new-file">
+
debian/tests/test-data/dsRNA_viruses.ags.gz
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<h4>Changes:</h4>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -13,12 +13,13 @@ Copyright: 1998-1999 Stephane Bortzmeyer <bortzmeyer@pasteur.fr></td>
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> 2001-2017 Aaron M. Ucko <ucko@debian.org></span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">Files: debian/tests/test-data<span class="idiff left right">/nc0305.aso.gz</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Files: debian/tests/test-data</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">Copyright: 1996-2018 NCBI </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext">Comment: GenBank Release 224.0</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> To dowload the file use:</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> To dowload the file<span class="idiff left right">s</span> use:</span>
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<td class="diff-line-num old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nih.gov/ncbi-asn1/daily-nc/nc0305.aso.gz</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/ASN_BINARY/Viruses/dsRNA_viruses.ags.gz</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">License: public_domain</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> The NCBI toolkit has been put into the public domain, completely unfettered:</span>
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<li id="d0b2adb0358f0eab7dd3bb1849dd4e795a81f242">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb#d0b2adb0358f0eab7dd3bb1849dd4e795a81f242"><strong>debian/source/include-binaries</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">debian/tests/test-data/nc0305.aso.gz</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">debian/tests/test-data/dsRNA_viruses.ags.gz</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/ncbi-tools6/commit/71bca8b826f3d0d2e28c6116e60fa385435197eb#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,7 +10,7 @@ fi</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: teal;">$AUTOPKGTEST_TMP</span></span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="shell">cp <span class="idiff left">/usr/share/doc/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff right">/test-data/nc0305.aso.gz</span> <span class="nb" style="color: #0086b3;">.</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="shell">cp <span class="nt" style="color: navy;"><span class="idiff left">-a</span></span><span class="idiff"> /usr/share/doc/</span><span class="k" style="font-weight: 600;"><span class="idiff">${</span></span><span class="nv" style="color: teal;"><span class="idiff">pkg</span></span><span class="k" style="font-weight: 600;"><span class="idiff">}</span></span><span class="idiff">/test-data/</span><span class="k" style="font-weight: 600;"><span class="idiff right">*</span></span> <span class="nb" style="color: #0086b3;">.</span></span>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell">gunzip <span class="k" style="font-weight: 600;">*</span></span>
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15
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"></span>
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16
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16
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---asn2all test---'</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="48" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -48,3 +48,26 @@ echo '---asnval test---'</td>
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48
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48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="shell">/usr/bin/asnval <span class="nt" style="color: navy;">-i</span> nc0305.aso <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-o</span> nc0305.val</span>
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49
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49
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-f</span> nc0305.val <span class="o" style="font-weight: 600;">]</span></span>
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50
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50
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="o" style="font-weight: 600;">!</span> <span class="nt" style="color: navy;">-s</span> nc0305.val <span class="o" style="font-weight: 600;">]</span> <span class="c" style="color: #998; font-style: italic;"># empty</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="shell"></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---cleanasn test---'</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="shell">/usr/bin/cleanasn <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-a</span> t <span class="nt" style="color: navy;">-D</span> t <span class="nt" style="color: navy;">-i</span> nc0305.aso <span class="nt" style="color: navy;">-o</span> nc0305_cleaned.aso</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> nc0305_cleaned.aso <span class="o" style="font-weight: 600;">]</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="shell"></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---debruijn test---'</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="shell">/usr/bin/debruijn <span class="nt" style="color: navy;">-a</span> ncbistdaa <span class="nt" style="color: navy;">-n</span> 4 <span class="o" style="font-weight: 600;">></span> debruijn.output</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> debruijn.output <span class="o" style="font-weight: 600;">]</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---gene2xml test---'</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="shell">/usr/bin/gene2xml <span class="nt" style="color: navy;">-b</span> <span class="nt" style="color: navy;">-i</span> dsRNA_viruses.ags <span class="nt" style="color: navy;">-o</span> dsRNA_viruses.xgs</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> dsRNA_viruses.xgs <span class="o" style="font-weight: 600;">]</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="shell"></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="shell"><span class="nb" style="color: #0086b3;">grep</span> <span class="s1" style="color: #d14;">'GI:'</span> nc0305.gbk | head | sed <span class="s1" style="color: #d14;">'s/.*GI://'</span> <span class="o" style="font-weight: 600;">></span> GIs.txt</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># insdseqget and idfetch testing requires internet connection. Comment lines below</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="shell"><span class="c" style="color: #998; font-style: italic;"># to skip the testing.</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---insdseqget test---'</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="shell">/usr/bin/insdseqget <span class="nt" style="color: navy;">-n</span> <span class="nt" style="color: navy;">-i</span> GIs.txt <span class="o" style="font-weight: 600;">></span> insdset.xml</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> insdset.xml <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="shell"><span class="nb" style="color: #0086b3;">echo</span> <span class="s1" style="color: #d14;">'---idfetch test---'</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="shell">/usr/bin/idfetch <span class="nt" style="color: navy;">-G</span> GIs.txt <span class="nt" style="color: navy;">-t</span> 2 <span class="nt" style="color: navy;">-o</span> idfetch.aso</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="shell"><span class="o" style="font-weight: 600;">[</span> <span class="nt" style="color: navy;">-s</span> idfetch.aso <span class="o" style="font-weight: 600;">]</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="shell"></span></pre>
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