Mercurial > repos > crs4 > edge_pro
annotate tool_dependencies.xml @ 4:d5464c9e1723 draft
Add support for paired collection of FASTQ (thanks to Inge Alexander Raknes).
| author | crs4 |
|---|---|
| date | Tue, 17 Mar 2015 10:44:33 -0400 |
| parents | ddcbf8732706 |
| children |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
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f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
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3 <package name="bowtie2" version="2.1.0"> |
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3
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
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4 <repository changeset_revision="017a00c265f1" name="package_bowtie2_2_1_0" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" /> |
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1
f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
parents:
0
diff
changeset
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5 </package> |
| 0 | 6 <package name="edge-pro" version="1.3.1"> |
| 7 <install version="1.0"> | |
| 8 <actions> | |
| 9 <action type="download_by_url">http://ccb.jhu.edu/software/EDGE-pro/EDGE_pro_v1.3.1.tar.gz</action> | |
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3
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
1
diff
changeset
|
10 <!-- Search executables in PATH instead of the CWD --> |
|
ddcbf8732706
Fix edge-pro tool dependency (uninstall and install again the tool dependency if you were encountering errors like 'Can't exec "./bowtie2-build": No such file or directory'). Update Orione citation.
crs4
parents:
1
diff
changeset
|
11 <action type="shell_command">sed -i -e 's|$sourceDir/||' edge.pl</action> |
| 0 | 12 <action type="shell_command">make</action> |
| 13 <action type="move_file"> | |
| 14 <source>count</source> | |
| 15 <destination>$INSTALL_DIR/bin</destination> | |
| 16 </action> | |
| 17 <action type="move_file"> | |
| 18 <source>edge.pl</source> | |
| 19 <destination>$INSTALL_DIR/bin</destination> | |
| 20 </action> | |
| 21 <action type="set_environment"> | |
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1
f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
parents:
0
diff
changeset
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22 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> |
| 0 | 23 </action> |
| 24 </actions> | |
| 25 </install> | |
| 26 <readme> | |
| 27 Dependencies of EDGE-pro which needs to be installed separately: | |
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1
f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
parents:
0
diff
changeset
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28 - Switch Perl module ( http://search.cpan.org/~rgarcia/Switch/Switch.pm ). |
|
f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
parents:
0
diff
changeset
|
29 |
|
f77ce4f92b46
Use $GALAXY_SLOTS instead of $EDGE_PRO_SITE_OPTIONS. Add dependency on bowtie2. Add readme.rst .
crs4
parents:
0
diff
changeset
|
30 Configuration: Previously (until Release 0), the EDGE_PRO_SITE_OPTIONS variable in the installed env.sh file was used to adjust the number of threads to use (--num-threads). This is not used anymore and may be removed. |
| 0 | 31 </readme> |
| 32 </package> | |
| 33 </tool_dependency> |