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Andrius Merkys pushed to branch master at <a href="https://salsa.debian.org/med-team/ncbi-igblast">Debian Med / ncbi-igblast</a>
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Commits:
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-igblast/-/commit/ed5814e3ace17b8b94eedfc5be6947cfa3eff51a">ed5814e3</a></strong>
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<span> by Andrius Merkys </span> <i> at 2025-03-04T17:35:16+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Check if directory before cd'ing.
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<strong style="font-weight: 600;"><a href="https://salsa.debian.org/med-team/ncbi-igblast/-/commit/3de90b715f037436cc4899ef9167298bbd00539d">3de90b71</a></strong>
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<span> by Andrius Merkys </span> <i> at 2025-03-05T10:06:44+02:00 </i>
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<pre class="commit-message" style='white-space: pre-wrap; display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: #fbfafd; border-radius: 2px; margin: 0; padding: 8px 12px; border: 1px solid #dcdcde;'>Subdirectory internal_data/ has to stay for igblast to find its files without patching.
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2 changed files:
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<a href="#38aa1cc0fe3572a67974c07272dafe6ab79baaaa">
debian/igblast.install
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debian/rules
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Changes:
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<a href="https://salsa.debian.org/med-team/ncbi-igblast/-/compare/727b720e6ef15b7a7a06fe352f57b3abd980b449...3de90b715f037436cc4899ef9167298bbd00539d#38aa1cc0fe3572a67974c07272dafe6ab79baaaa"><strong style="font-weight: 600;">debian/igblast.install</strong></a>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC1" class="line" lang="php"><span class="n" style="color: #333333;">c</span><span class="o" style="font-weight: 600;">++/</span><span class="no" style="color: #008080;">GCC</span><span class="o" style="font-weight: 600;">*/</span><span class="n" style="color: #333333;">bin</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span><span class="o" style="font-weight: 600;">*</span> <span class="n" style="color: #333333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">bin</span></span>
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC2" class="line" lang="php"><span class="n" style="color: #333333;">c</span><span class="o" style="font-weight: 600;">++/</span><span class="n" style="color: #333333;">src</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">app</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">edit_imgt_file</span><span class="mf" style="color: #009999;">.</span><span class="n" style="color: #333333;">pl</span> <span class="n" style="color: #333333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">bin</span></span>
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC3" class="line" lang="php"><span class="n" style="color: #333333;">c</span><span class="o" style="font-weight: 600;">++/</span><span class="n" style="color: #333333;">src</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">app</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">internal_data</span><span class="o" style="font-weight: 600;"><span class="idiff left right deletion" style="background-color: #fac5cd;">/*</span></span> <span class="n" style="color: #333333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">ncbi</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span></span></pre></td>
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC3" class="line" lang="php"><span class="n" style="color: #333333;">c</span><span class="o" style="font-weight: 600;">++/</span><span class="n" style="color: #333333;">src</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">app</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">internal_data</span> <span class="n" style="color: #333333;">usr</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">share</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">ncbi</span><span class="o" style="font-weight: 600;">/</span><span class="n" style="color: #333333;">igblast</span></span></pre></td>
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<a href="https://salsa.debian.org/med-team/ncbi-igblast/-/compare/727b720e6ef15b7a7a06fe352f57b3abd980b449...3de90b715f037436cc4899ef9167298bbd00539d#8756c63497c8dc39f7773438edf53b220c773f67"><strong style="font-weight: 600;">debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">...</td>
<td class="line_content match" style="color: rgba(5,5,6,.24); padding: inherit;" bgcolor="#fbfafd">@@ -35,7 +35,7 @@ override_dh_clean:</td>
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<td class="new_line diff-line-num" data-linenumber="35" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC35" class="line" lang="plaintext"> #or there may be none but then there is still a module named after the</span>
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<td class="old_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="36" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
36
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC36" class="line" lang="plaintext"> #directory. Clean everything!</span>
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<td class="old_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="37" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC37" class="line" lang="plaintext"> -for x in c++/src/objects/* ; do \</span>
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<td class="old_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
38
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<td class="new_line diff-line-num old" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: inherit;" align="right" bgcolor="#f9d7dc">
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<td class="line_content old" style="padding: inherit;" bgcolor="#fbe9eb"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>-<span id="LC38" class="line" lang="plaintext"> (<span class="idiff left right deletion" style="background-color: #fac5cd;">c</span>d "$$x" && ( \</span>
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<td class="old_line diff-line-num new" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="38" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: inherit;" align="right" bgcolor="#ddfbe6">
38
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<td class="line_content new" style="padding: inherit;" bgcolor="#ecfdf0"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'>+<span id="LC38" class="line" lang="plaintext"> (<span class="idiff left addition" style="background-color: #c7f0d2;">test -</span>d "$$x" <span class="idiff right addition" style="background-color: #c7f0d2;">&& cd "$$x"</span> && ( \</span>
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<td class="old_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="39" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
39
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC39" class="line" lang="plaintext"> mods="`echo *.module`" ; \</span>
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<td class="old_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="new_line diff-line-num" data-linenumber="40" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC40" class="line" lang="plaintext"> [ "$${mods#*\*}" = "$$mods" ] || mods="`basename $$x`" ; \</span>
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41
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<td class="new_line diff-line-num" data-linenumber="41" style="width: 35px; color: rgba(5,5,6,.24); border-right-width: 1px; border-right-color: #ececef; border-right-style: solid; padding: inherit;" align="right" bgcolor="#fbfafd">
41
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<td class="line_content" style="padding: inherit;"><pre style='display: block; font-size: 14px; color: #3a383f; position: relative; font-family: "GitLab Mono", "JetBrains Mono", "Menlo", "DejaVu Sans Mono", "Liberation Mono", "Consolas", "Ubuntu Mono", "Courier New", "andale mono", "lucida console", monospace; font-variant-ligatures: none; word-break: break-all; word-wrap: break-word; background-color: inherit; border-radius: 2px; margin: 0; padding: 0; border: inherit solid #dcdcde;'> <span id="LC41" class="line" lang="plaintext"> for mod in $$mods ; do \</span>
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