Mercurial > repos > gga > genenotebook_genenotebook_build
comparison macros.xml @ 8:29eeddd8ea62 draft
planemo upload for repository https://github.com/galaxy-genome-annotation/galaxy-tools/tree/master/tools/genenotebook commit 1429f00733ee24bf2edf56b9fd7ff4ad2dec3f15
author | gga |
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date | Tue, 20 Feb 2024 10:05:05 +0000 |
parents | dfb2bc3aedbd |
children | e98f93ba54cd |
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7:dfb2bc3aedbd | 8:29eeddd8ea62 |
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5 <requirement type="package" version="@TOOL_VERSION@">genoboo</requirement> | 5 <requirement type="package" version="@TOOL_VERSION@">genoboo</requirement> |
6 <yield/> | 6 <yield/> |
7 </requirements> | 7 </requirements> |
8 </xml> | 8 </xml> |
9 | 9 |
10 <token name="@TOOL_VERSION@">0.4.12</token> | 10 <token name="@TOOL_VERSION@">0.4.13</token> |
11 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> | 11 <token name="@WRAPPER_VERSION@">@TOOL_VERSION@+galaxy0</token> |
12 | 12 |
13 <xml name="citation"> | 13 <xml name="citation"> |
14 <citations> | 14 <citations> |
15 <citation type="doi">10.1093/bioinformatics/btz491</citation> | 15 <citation type="doi">10.1093/bioinformatics/btz491</citation> |
35 This runs GeneNoteBook, and a local mongodb server listening only on a unix socket, created in the work dir. | 35 This runs GeneNoteBook, and a local mongodb server listening only on a unix socket, created in the work dir. |
36 The bind_ip option is a trick to prevent mongod from opening a TCP socket. | 36 The bind_ip option is a trick to prevent mongod from opening a TCP socket. |
37 For some unknwon reason, unixSocketPrefix needs an absolute path | 37 For some unknwon reason, unixSocketPrefix needs an absolute path |
38 --> | 38 --> |
39 <token name="@START_GNB@"><![CDATA[ | 39 <token name="@START_GNB@"><![CDATA[ |
40 export GNB_PORT="\$(bash '$__tool_directory__/find_free_port.sh')"; | |
41 export MONGO_URI="\$(pwd | sed 's|/|%2F|g')"; | 40 export MONGO_URI="\$(pwd | sed 's|/|%2F|g')"; |
42 #if $existing | 41 #if $existing |
43 tar -xf '${existing}' mongo_db; | 42 tar -xf '${existing}' mongo_db; |
44 #else | 43 #else |
45 mkdir ./mongo_db/; | 44 mkdir ./mongo_db/; |