Mercurial > repos > devteam > package_samtools_0_1_16
annotate tool_dependencies.xml @ 1:3cc494fb5a14 draft default tip
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
| author | devteam |
|---|---|
| date | Wed, 25 Sep 2013 10:50:18 -0400 |
| parents | 75367f13eb3c |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
| 3 <package name="samtools" version="0.1.16"> | |
| 4 <install version="1.0"> | |
|
1
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
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5 <actions_group> |
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3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
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6 <actions os="linux" architecture="i386"> |
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3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
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7 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action> |
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3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
8 <action type="move_directory_files"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
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9 <source_directory>.</source_directory> |
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3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
10 <destination_directory>$INSTALL_DIR</destination_directory> |
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3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
11 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
12 </actions> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
13 <actions os="linux" architecture="x86_64"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
14 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
15 <action type="move_directory_files"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
16 <source_directory>.</source_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
17 <destination_directory>$INSTALL_DIR</destination_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
18 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
19 </actions> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
20 <actions os="darwin" architecture="i386"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
21 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
22 <action type="move_directory_files"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
23 <source_directory>.</source_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
24 <destination_directory>$INSTALL_DIR</destination_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
25 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
26 </actions> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
27 <actions os="darwin" architecture="x86_64"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
28 <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
29 <action type="move_directory_files"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
30 <source_directory>.</source_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
31 <destination_directory>$INSTALL_DIR</destination_directory> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
32 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
33 </actions> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
34 <actions> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
35 <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
36 <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
37 <action type="shell_command">make</action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
38 <action type="move_file"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
39 <source>samtools</source> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
40 <destination>$INSTALL_DIR/bin</destination> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
41 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
42 <action type="move_file"> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
43 <source>libbam.a</source> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
44 <destination>$INSTALL_DIR/lib</destination> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
45 </action> |
|
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
46 </actions> |
| 0 | 47 <action type="set_environment"> |
| 48 <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> | |
|
1
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
49 <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable> |
| 0 | 50 </action> |
|
1
3cc494fb5a14
Uploaded an updated tool_dependencies.xml that first attempts to download a precompiled binary for SAMTools 0.1.16.
devteam
parents:
0
diff
changeset
|
51 </actions_group> |
| 0 | 52 </install> |
| 53 <readme> | |
| 54 This is the last version of SAMTools to include the 'pileup' command. | |
| 55 | |
| 56 Program: samtools (Tools for alignments in the SAM format) | |
| 57 Version: 0.1.16 (r963:234) | |
| 58 | |
| 59 Usage: samtools <command> [options] | |
| 60 | |
| 61 Command: view SAM<->BAM conversion | |
| 62 sort sort alignment file | |
| 63 pileup generate pileup output | |
| 64 mpileup multi-way pileup | |
| 65 depth compute the depth | |
| 66 faidx index/extract FASTA | |
| 67 tview text alignment viewer | |
| 68 index index alignment | |
| 69 idxstats BAM index stats (r595 or later) | |
| 70 fixmate fix mate information | |
| 71 glfview print GLFv3 file | |
| 72 flagstat simple stats | |
| 73 calmd recalculate MD/NM tags and '=' bases | |
| 74 merge merge sorted alignments | |
| 75 rmdup remove PCR duplicates | |
| 76 reheader replace BAM header | |
| 77 cat concatenate BAMs | |
| 78 targetcut cut fosmid regions (for fosmid pool only) | |
| 79 phase phase heterozygotes | |
| 80 </readme> | |
| 81 </package> | |
| 82 </tool_dependency> |