Mercurial > repos > crs4 > prokka
annotate tool_dependencies.xml @ 2:4bafaa074484 draft
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
| author | crs4 |
|---|---|
| date | Fri, 25 Oct 2013 08:59:51 -0400 |
| parents | 4b6f16a79fe4 |
| children | fffa1ae330ae |
| rev | line source |
|---|---|
| 0 | 1 <?xml version="1.0"?> |
| 2 <tool_dependency> | |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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3 <package name="blast+" version="2.2.28"> |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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4 <repository changeset_revision="ed85ca8e4295" name="package_blast_plus_2_2_28" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> |
| 0 | 5 </package> |
| 6 <package name="hmmer" version="3.1b1"> | |
| 7 <repository changeset_revision="007c736bf7e8" name="package_hmmer_3_1" owner="lionelguy" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
| 8 </package> | |
| 9 <package name="aragorn" version="1.2.36"> | |
| 10 <repository changeset_revision="f09e2902e6ed" name="package_aragorn_1_2_36" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
| 11 </package> | |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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12 <package name="prodigal" version="2.60"> |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
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13 <repository changeset_revision="acf0e8b718c9" name="package_prodigal_2_60" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> |
|
4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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14 </package> |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
parents:
1
diff
changeset
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15 <package name="barrnap" version="0.2"> |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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16 <repository changeset_revision="8ab7a17861ea" name="package_barrnap_0_2" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> |
|
4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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17 </package> |
| 0 | 18 <package name="infernal" version="1.1rc4"> |
| 19 <repository changeset_revision="b9cc978bc83b" name="package_infernal_1_1rc4" owner="iuc" toolshed="http://toolshed.g2.bx.psu.edu" /> | |
| 20 </package> | |
| 21 <package name="prokka" version="1.7"> | |
| 22 <install version="1.0"> | |
| 23 <actions> | |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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24 <action type="download_by_url">http://www.vicbioinformatics.com/prokka-1.7.tar.gz</action> |
| 0 | 25 <action type="move_directory_files"> |
| 26 <source_directory>.</source_directory> | |
| 27 <destination_directory>$INSTALL_DIR</destination_directory> | |
| 28 </action> | |
| 29 <action type="set_environment"> | |
| 30 <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable> | |
| 31 </action> | |
| 32 <action type="set_environment"> | |
| 33 <environment_variable action="set_to" name="PROKKA_SITE_OPTIONS">"--cpus 8"</environment_variable> | |
| 34 </action> | |
| 35 </actions> | |
| 36 </install> | |
| 37 <readme> | |
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2
4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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38 Warning: Prokka includes custom databases and is thus about a 2.0 GB download! |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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1
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39 |
| 0 | 40 Dependencies of Prokka which needs to be installed separately: |
| 41 - Perl core modules: File::Copy, FindBin, Getopt::Long, List::Util, Scalar::Util, Time::Piece, Time::Seconds; | |
| 1 | 42 - Perl modules: Bio::SeqIO from BioPerl ( http://search.cpan.org/dist/BioPerl/ ) >= 1.6.900, XML::Simple ( http://search.cpan.org/dist/XML-Simple/ ); |
| 0 | 43 - Prodigal ( http://prodigal.ornl.gov/ ) >= 2.60 ; |
| 44 - tbl2asn ( http://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ) >= 21.0 ; | |
| 1 | 45 - GNU Parallel ( http://www.gnu.org/software/parallel/ ) >= 20130422 ; |
| 0 | 46 - Barrnap ( http://www.vicbioinformatics.com/software.barrnap.shtml ) >= 0.1 . |
| 47 | |
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4bafaa074484
Merge with Lionel Guy's wrapper. Directly call prokka, remove prokka.py . Add locustag, increment, gffver, compliant, addgenes, genus, species, strain, plasmid, gcode, usegenus, metagenome, fast, evalue, norrna, notrna params. Update BLAST+ dependency to 2.2.28. Add dependencies on prodigal and barrnap. Add readme.rst .
crs4
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48 Configuration: Change the PROKKA_SITE_OPTIONS variable in the installed env.sh file to adjust the number of CPUs to use (--cpus). |
| 0 | 49 </readme> |
| 50 </package> | |
| 51 </tool_dependency> |