Mercurial > repos > peterjc > ncbi_blast_plus
changeset 21:6902315b7730 draft
Uploaded v0.0.20pre12, try downloading platform specific binaries
| author | peterjc |
|---|---|
| date | Mon, 05 Aug 2013 12:39:59 -0400 |
| parents | 688f3fb09a6a |
| children | 9b8b2817f411 |
| files | ncbi_blast_plus/ncbi_makeblastdb.xml ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml ncbi_blast_plus/tool_dependencies.xml |
| diffstat | 3 files changed, 89 insertions(+), 73 deletions(-) [+] |
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--- a/ncbi_blast_plus/ncbi_makeblastdb.xml Tue Jul 30 07:33:46 2013 -0400 +++ b/ncbi_blast_plus/ncbi_makeblastdb.xml Mon Aug 05 12:39:59 2013 -0400 @@ -1,5 +1,5 @@ <tool id="ncbi_makeblastdb" name="NCBI BLAST+ makeblastdb" version="0.0.5"> - <description>Make BLAST database</description> + <description>Make BLAST database</description> <requirements> <requirement type="binary">makeblastdb</requirement> <requirement type="package" version="2.2.26+">blast+</requirement> @@ -14,7 +14,8 @@ ## some extra spaces, e.g. -in " file1 file2 file3 " but BLAST seems happy: -in " #for $i in $in -${i.file} #end for +${i.file} +#end for " #if $title: -title "$title" @@ -38,71 +39,73 @@ ## #else if $tax.select == 'map': ## -taxid_map $tax.map ## #end if -</command> -<stdio> - <!-- Anything other than zero is an error --> - <exit_code range="1:" /> - <exit_code range=":-1" /> - <!-- In case the return code has not been set propery check stderr too --> - <regex match="Error:" /> - <regex match="Exception:" /> -</stdio> -<inputs> - <param name="dbtype" type="select" display="radio" label="Molecule type of input"> - <option value="prot">protein</option> - <option value="nucl">nucleotide</option> - </param> - <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) - <repeat name="in" title="Blast or Fasta Database" min="1"> - <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="Blast or Fasta database" /> - </repeat> - --> - <repeat name="in" title="FASTA file" min="1"> - <param name="file" type="data" format="fasta" /> - </repeat> - <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> - <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> - <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> + </command> + <stdio> + <!-- Anything other than zero is an error --> + <exit_code range="1:" /> + <exit_code range=":-1" /> + <!-- In case the return code has not been set propery check stderr too --> + <regex match="Error:" /> + <regex match="Exception:" /> + </stdio> + <inputs> + <param name="dbtype" type="select" display="radio" label="Molecule type of input"> + <option value="prot">protein</option> + <option value="nucl">nucleotide</option> + </param> + <!-- TODO Allow merging of existing BLAST databases (conditional on the database type) + <repeat name="in" title="BLAST or FASTA Database" min="1"> + <param name="file" type="data" format="fasta,blastdbn,blastdbp" label="BLAST or FASTA database" /> + </repeat> + --> + <repeat name="in" title="FASTA file" min="1"> + <param name="file" type="data" format="fasta" /> + </repeat> + <param name="title" type="text" value="" label="Title for BLAST database" help="This is the database name shown in BLAST search output" /> + <param name="parse_seqids" type="boolean" truevalue="-parse_seqids" falsevalue="" checked="False" label="Parse the sequence identifiers" help="This is only advised if your FASTA file follows the NCBI naming conventions using pipe '|' symbols" /> + <param name="hash_index" type="boolean" truevalue="-hash_index" falsevalue="" checked="true" label="Enable the creation of sequence hash values." help="These hash values can then be used to quickly determine if a given sequence data exists in this BLAST database." /> - <!-- SEQUENCE MASKING OPTIONS --> - <!-- TODO - <repeat name="mask_data" title="Provide one or more files containing masking data"> - <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> - </repeat> - <repeat name="gi_mask" title="Create GI indexed masking data"> - <param name="file" type="data" format="asnb" label="Masking data output file" /> - </repeat> - --> + <!-- SEQUENCE MASKING OPTIONS --> + <!-- TODO + <repeat name="mask_data" title="Provide one or more files containing masking data"> + <param name="file" type="data" format="asnb" label="File containing masking data" help="As produced by NCBI masking applications (e.g. dustmasker, segmasker, windowmasker)" /> + </repeat> + <repeat name="gi_mask" title="Create GI indexed masking data"> + <param name="file" type="data" format="asnb" label="Masking data output file" /> + </repeat> + --> - <!-- TAXONOMY OPTIONS --> - <!-- TODO - <conditional name="tax"> - <param name="select" type="select" label="Taxonomy options"> - <option value="">Do not assign sequences to Taxonomy IDs</option> - <option value="id">Assign all sequences to one Taxonomy ID</option> - <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> - </param> - <when value=""> - </when> - <when value="id"> - <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> - </when> - <when value="map"> - <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> - </when> - </conditional> - --> -</inputs> -<outputs> - <!-- If we only accepted one FASTA file, we could use its human name here... --> - <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> - <change_format> - <when input="dbtype" value="nucl" format="blastdbn"/> - <when input="dbtype" value="prot" format="blastdbp"/> - </change_format> - </data> -</outputs> -<help> + <!-- TAXONOMY OPTIONS --> + <!-- TODO + <conditional name="tax"> + <param name="select" type="select" label="Taxonomy options"> + <option value="">Do not assign sequences to Taxonomy IDs</option> + <option value="id">Assign all sequences to one Taxonomy ID</option> + <option value="map">Supply text file mapping sequence IDs to taxnomy IDs</option> + </param> + <when value=""> + </when> + <when value="id"> + <param name="id" type="integer" value="" label="NCBI taxonomy ID" help="Integer >=0" /> + </when> + <when value="map"> + <param name="file" type="data" format="txt" label="Seq ID : Tax ID mapping file" help="Format: SequenceId TaxonomyId" /> + </when> + </conditional> + --> + </inputs> + <outputs> + <!-- If we only accepted one FASTA file, we could use its human name here... --> + <data name="outfile" format="data" label="${dbtype.value_label} BLAST database from ${on_string}"> + <change_format> + <when input="dbtype" value="nucl" format="blastdbn" /> + <when input="dbtype" value="prot" format="blastdbp" /> + </change_format> + </data> + </outputs> + <tests> + </tests> + <help> **What it does** Make BLAST database from one or more FASTA files and/or BLAST databases. @@ -125,5 +128,5 @@ This wrapper is available to install into other Galaxy Instances via the Galaxy Tool Shed at http://toolshed.g2.bx.psu.edu/view/devteam/ncbi_blast_plus -</help> + </help> </tool>
--- a/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Tue Jul 30 07:33:46 2013 -0400 +++ b/ncbi_blast_plus/ncbi_rpstblastn_wrapper.xml Mon Aug 05 12:39:59 2013 -0400 @@ -19,13 +19,13 @@ #end if -evalue $evalue_cutoff -out "$output1" -##Set the extended list here so if/when we add things, saved workflows are not affected +## Set the extended list here so if/when we add things, saved workflows are not affected #if str($out_format)=="ext": -outfmt "6 std sallseqid score nident positive gaps ppos qframe sframe qseq sseq qlen slen" #else: -outfmt $out_format #end if -##Seems rpstblastn does not currently support multiple threads :( +## rpstblastn does not support multiple threads up to release 2.2.27+. Added in BLAST 2.2.28+. ##-num_threads 8 #if $adv_opts.adv_opts_selector=="advanced": $adv_opts.filter_query
--- a/ncbi_blast_plus/tool_dependencies.xml Tue Jul 30 07:33:46 2013 -0400 +++ b/ncbi_blast_plus/tool_dependencies.xml Mon Aug 05 12:39:59 2013 -0400 @@ -3,16 +3,29 @@ <package name="blast+" version="2.2.26+"> <install version="1.0"> <actions> - <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-src.tar.gz</action> - <action type="shell_command">cd c++ && ./configure --prefix=$INSTALL_DIR && make && make install</action> + <action type="download_by_url"> + <url_template os="linux" architecture="x86_64">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</url_template> + <url_template os="linux" architecture="i386">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> + <url_template os="linux" architecture="i686">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</url_template> + <url_template os="darwin">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</url_template> + </action> + <action type="move_directory_files"> + <!-- Galaxy will have changed directory into ncbi-blast-2.2.26+/ --> + <source_directory>bin</source_directory> + <destination_directory>$INSTALL_DIR</destination_directory> + </action> <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> </action> </actions> </install> <readme> -Downloads and compiles BLAST+ from the NCBI, which assumes you have -all the required build dependencies installed. See: +Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+ +binaries from the NCBI, which is faster than performing a local compliation, +avoids any issues with build dependencies, and is more reproducible between +installations as there is no variability from the compiler or library versions. + +For more details, see: http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs&DOC_TYPE=Download </readme> </package>