| Previous changeset 0:cc6db1ee2d48 (2015-10-05) Next changeset 2:79feb4eb7832 (2015-11-18) |
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Commit message:
Uploaded |
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added:
Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Galaxy-Workflow-workflow_gandalf_3.0.ga repository_dependencies.xml |
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removed:
mdust.xml mdust_wrapper.py test-data/masked-seq-mdust.fsa test-data/seq-mdust.fsa tool_dependencies.xml |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a Galaxy-Workflow-creation_workflow_gandalf_2.0.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-creation_workflow_gandalf_2.0.ga Wed Nov 18 09:16:05 2015 -0500 |
| [ |
| b'@@ -0,0 +1,384 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "creation workflow gandalf 2.0", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 288, \n+ "top": 200\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 288, \n+ "top": 285\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ 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"type": "vcf"\n+ }, \n+ {\n+ "name": "output_html", \n+ "type": "html"\n+ }\n+ ], \n+ "position": {\n+ "left": 1904, \n+ "top": 265\n+ }, \n+ "post_job_actions": {\n+ "RenameDatasetActionoutputVCF": {\n+ "action_arguments": {\n+ "newname": "#{inputVCF | basename}.filteredVCF"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "outputVCF"\n+ }, \n+ "RenameDatasetActionoutput_html": {\n+ "action_arguments": {\n+ "newname": "#{inputVCF | basename}.VCFFiltering.graphs"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "output_html"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFFiltering/0.01", \n+ "tool_state": "{\\"inputVCF\\": \\"null\\", \\"BedFile_List\\": \\"{\\\\\\"BedFiles\\\\\\": [{\\\\\\"__index__\\\\\\": 0, \\\\\\"inputBed\\\\\\": null}], \\\\\\"is_BedFile\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 1}\\", \\"AF\\": \\"\\\\\\"0.9\\\\\\"\\", \\"__page__\\": 0, \\"DP_auto\\": \\"{\\\\\\"is_DP_auto\\\\\\": \\\\\\"True\\\\\\", \\\\\\"__current_case__\\\\\\": 0}\\", \\"__rerun_remap_job_id__\\": null, \\"AN\\": \\"\\\\\\"2\\\\\\"\\", \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\"}", \n+ "tool_version": "0.01", \n+ "type": "tool", \n+ "user_outputs": []\n+ }\n+ }, \n+ "uuid": "7ffb6371-3f23-4cfe-8c68-70019963aa4a"\n+}\n\\ No newline at end of file\n' |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a Galaxy-Workflow-workflow_gandalf_3.0.ga --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/Galaxy-Workflow-workflow_gandalf_3.0.ga Wed Nov 18 09:16:05 2015 -0500 |
| [ |
| b'@@ -0,0 +1,933 @@\n+{\n+ "a_galaxy_workflow": "true", \n+ "annotation": "", \n+ "format-version": "0.1", \n+ "name": "workflow gandalf 3.0", \n+ "steps": {\n+ "0": {\n+ "annotation": "", \n+ "id": 0, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 258, \n+ "top": 593\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": "data_input", \n+ "user_outputs": []\n+ }, \n+ "1": {\n+ "annotation": "", \n+ "id": 1, \n+ "input_connections": {}, \n+ "inputs": [\n+ {\n+ "description": "", \n+ "name": "Input Dataset"\n+ }\n+ ], \n+ "name": "Input dataset", \n+ "outputs": [], \n+ "position": {\n+ "left": 258, \n+ "top": 685\n+ }, \n+ "tool_errors": null, \n+ "tool_id": null, \n+ "tool_state": "{\\"name\\": \\"Input Dataset\\"}", \n+ "tool_version": null, \n+ "type": 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"outputVCFStorage"\n+ }, \n+ "RenameDatasetActionoutputVCFStorage": {\n+ "action_arguments": {\n+ "newname": "#{inputFasta | basename}.matrix"\n+ }, \n+ "action_type": "RenameDatasetAction", \n+ "output_name": "outputVCFStorage"\n+ }\n+ }, \n+ "tool_errors": null, \n+ "tool_id": "toolshed.g2.bx.psu.edu/repos/urgi-team/vcfgandalftools/VCFStorage/0.01", \n+ "tool_state": "{\\"__page__\\": 0, \\"chromInfo\\": \\"\\\\\\"/home/galaxy-dev/galaxy-dist/tool-data/shared/ucsc/chrom/?.len\\\\\\"\\", \\"__rerun_remap_job_id__\\": null, \\"VCFFile\\": \\"[{\\\\\\"strainName\\\\\\": \\\\\\"strain1\\\\\\", \\\\\\"__index__\\\\\\": 0, \\\\\\"inputStrainVCF\\\\\\": null}, {\\\\\\"strainName\\\\\\": \\\\\\"strain2\\\\\\", \\\\\\"__index__\\\\\\": 1, \\\\\\"inputStrainVCF\\\\\\": null}]\\", \\"inputFasta\\": \\"null\\"}", \n+ "tool_version": "0.01", \n+ "type": "tool", \n+ "user_outputs": []\n+ }, \n+ "19": {\n+ "annotation": "", \n+ "id": 19, \n+ "input_connections": {\n+ "inputTabular": {\n+ "id": 18, 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| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a mdust.xml --- a/mdust.xml Mon Oct 05 11:05:21 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,87 +0,0 @@ -<?xml version="1.0"?> -<tool id="mdust" name="mdust" version="1.0"> - <description>fast and symmetric DUST implementation to mask low-complexity DNA sequences</description> - <requirements> - <requirement type="package" version="1.0">mdust</requirement> - </requirements> - <command interpreter="python"> - mdust_wrapper.py -i ${input_file} -v ${cutoff} -w ${wsize} -m ${masking_letter.masking_letter_selector} -f ${output_type.output_type_selector} - - #if str( $output_type.output_type_selector) == "default" - -o ${output_masked_fasta} - #end if - - #if str( $output_type.output_type_selector) == "tab" - -o ${output_tab} - #end if - - #if str( $output_type.output_type_selector) == "bed" - -o ${output_bed} - #end if - </command> - <inputs> - <param name="input_file" type="data" format="fasta" label="Input fasta file" help=""/> - <param name="cutoff" type="integer" value="28" label="cutt-off" help="cut-off" /> - <param name="wsize" type="integer" value="3" label="set maximum word size" help="word-size" /> - <conditional name="masking_letter"> - <param name="masking_letter_selector" type="select" label="Choose your masking type" help="Select the masking letter (N,X or lowercase)" > - <option value="N" selected="True">N (default)</option> - <option value="X">X</option> - <option value="L">lowercase</option> - </param> - </conditional> - <conditional name="output_type"> - <param name="output_type_selector" type="select" label="Choose your output type" help="select your output"> - <option value="default" selected="True">masked file (default)</option> - <option value="tab">output masking coordinates only (tab delimited)</option> - <option value="bed">output masking coordinates only (bed format)</option> - </param> - </conditional> - </inputs> - <outputs> - <data format="fasta" name="output_masked_fasta" label="masked.${input_file.name}"> - <filter>( output_type['output_type_selector'] == 'default' )</filter> - </data> - <data format="tabular" name="output_tab" label="${input_file.name}.tab"> - <filter>( output_type['output_type_selector'] == 'tab' )</filter> - </data> - <data format="bed" name="output_bed" label="${input_file.name}.bed"> - <filter>( output_type['output_type_selector'] == 'bed' )</filter> - </data> - </outputs> - <tests> - <test> - <param name="input_file" value="seq-mdust.fsa" /> - <output name="output_masked_fasta" file="masked-seq-mdust.fsa" ftype="fasta" /> - </test> - </tests> - <help><![CDATA[ -mdust new implementation of the DUST module that uses the same function to assign a complexity score to a sequence, but uses a different rule by which high-scoring sequences are masked. - ------ - -**Usage:** :: - - mdust [<fasta-file>] [-w <wsize>] [-v <cut-off>] [-m N|X|L] [-c] - if no <fasta-file> is given, a multi-fasta stream is expected at stdin - -v default <cut-off> value is 28 (lower values might mask more, - but possibly still useful sequence; > 64 will rarely mask poly-triplets) - -w set maximum word size to <wsize> (default 3) - -m if fasta output is not disabled by -c, set the masking letter type: - N ('N', default), X ('X'), L (make lowercase) - -c output masking coordinates only: - seq_name, seqlength, mask_start, mask_end (tab delimited) - ------ - -**Reference:** :: - - A fast and symmetric DUST implementation to mask low-complexity DNA sequences. - Morgulis A, Gertz EM, Schäffer AA, Agarwala R. - J Comput Biol. 2006 Jun;13(5):1028-40. - PMID:16796549 - - -]]> - </help> -</tool> |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a mdust_wrapper.py --- a/mdust_wrapper.py Mon Oct 05 11:05:21 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| [ |
| @@ -1,113 +0,0 @@ -#!/usr/bin/env python - -import subprocess -import tempfile -import sys -import os -import re -from optparse import OptionParser - - -class MdustWrapper(object): - - def __init__(self): - self._options = None - - def stop_err(self, msg): - sys.stderr.write("%s\n" % msg) - sys.exit() - - def setAttributesFromCmdLine(self): - description = "mdust_wrapper" - description += "\nWrapper for mdust\n" - description += "example: mdust_wrapper.py -i seq.fasta -v 27\n" - parser = OptionParser(description = description, version = "0.1") - parser.add_option("-i", "--input", dest = "FastaFile", action = "store", type = "string", help = "Input Fasta File name [compulsory] [format: Fasta]", default = "") - parser.add_option("-o", "--output", dest = "outFile", action = "store", type = "string", help = "output File name [compulsory] [format: fasta,tab or bed]", default = "") - parser.add_option("-v", "--cutoff", dest = "cutoff", action = "store", type = "int", help = "cutoff", default = 28) - parser.add_option("-w", "--wsize", dest = "wsize", action = "store", type = "int", help = "window size", default = 3) - parser.add_option("-m", "--maskingletter", dest = "maskingletter", action = "store", type = "string", help = "masking letter", default = "N") - parser.add_option("-f", "--format", dest = "format", action = "store", type = "string", help = "format", default = "default") - options = parser.parse_args()[0] - self._setAttributesFromOptions(options) - - - def _setAttributesFromOptions(self, options): - self._options = options - - if self._options.FastaFile == "": - raise Exception("Missing input file, please provide fasta file with -i file !") - if self._options.outFile == "": - raise Exception("Missing output file, please provide output file with -o file !") - - - def run(self): - - prg = "mdust" - args = "" - args += " %s" % self._options.FastaFile - args += " -v %d" % self._options.cutoff - args += " -w %d" % self._options.wsize - args += " -m %s" % self._options.maskingletter - if self._options.format == "tab" or self._options.format == "bed": - args += " -c " - cmd = "%s %s" %(prg, args) - - try: - tmp_err = tempfile.NamedTemporaryFile().name - tmp_out = "outfile" - tmp_stderr = open( tmp_err, 'wb' ) - tmp_stdout = open( tmp_out, 'wb' ) - proc = subprocess.Popen( args=cmd, shell=True, cwd=".", stdout=tmp_stdout, stderr=tmp_stderr ) - returncode = proc.wait() - tmp_stderr.close() - # get stderr, allowing for case where it's very large - tmp_stderr = open( tmp_err, 'rb' ) - tmp_stdout = open( tmp_out, 'rb' ) - - stderr = '' - stdout = '' - buffsize = 1048576 - try: - while True: - stdout += tmp_stdout.read( buffsize ) - if not stdout or len( stdout ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stdout.close() - - try: - while True: - stderr += tmp_stderr.read( buffsize ) - if not stderr or len( stderr ) % buffsize != 0: - break - except OverflowError: - pass - tmp_stderr.close() - if stderr: - raise Exception, stderr - except Exception, e: - self.stop_err( 'Error with mdust :\n' + str( e ) ) - - if self._options.format == 'bed': - with open(tmp_out,"r") as fin: - with open(self._options.outFile, "w") as fout: - lineNumber = 0 - for line in fin: - lineNumber += 1 - m = re.search(r"^(\S+)\t(\d+)\t(\d+)\t(\d+)$", line) - if m is not None: - fout.write("%s\t%d\t%d\n" % (m.group(1), int(m.group(3))-1, int(m.group(4)))) - if m is None: - raise Exception("\nLine %d '%s' does not has a mdust format." % (lineNumber, line)) - else: - os.rename(tmp_out,self._options.outFile) - - - - -if __name__ == "__main__": - iWrapper = MdustWrapper() - iWrapper.setAttributesFromCmdLine() - iWrapper.run() |
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| diff -r cc6db1ee2d48 -r 034d5b66e97a repository_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/repository_dependencies.xml Wed Nov 18 09:16:05 2015 -0500 |
| b |
| @@ -0,0 +1,10 @@ +<?xml version="1.0"?> +<repositories description="Gandalf worflow needed repository"> + <repository changeset_revision="d8c9597bfb09" name="bwa" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="74980f9f1ccc" name="mapqfilter" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="379fdf4c41ac" name="picard" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="874dd6c0fcde" name="freebayes4workflow" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="3552a8d9f51c" name="vcfgandalftools" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="af65bfb54977" name="suite_samtools_0_1_19" owner="devteam" toolshed="http://toolshed.g2.bx.psu.edu" /> + <repository changeset_revision="cc6db1ee2d48" name="mdust" owner="urgi-team" toolshed="http://toolshed.g2.bx.psu.edu" /> +</repositories> |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a test-data/masked-seq-mdust.fsa --- a/test-data/masked-seq-mdust.fsa Mon Oct 05 11:05:21 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5000 +0,0 @@\n->seqmdust\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN\n-NNNNcaccctcaccctCGgtcgtacggcgtgacaatgtctccagaatcgatttggtcttg\n-acgaaagcagcgcacatagcacttccggatgattttgtcgcatgctttgtcaaacacgac\n-gtccgtaagtactagctcgttcggcctagctttcgcgcccgtctgctgctcgctcttccg\n-caagaattgacgcagaacgacgcgccgcttctgggtatcgaactcgataatttgggctgg\n-ctggagccggtcctcgtcaaggtcgtcattccattcgcggacgaggacggtgtcaccaat\n-tgcatatttgctccggcactcgtcgaatataggaacgtcatgcttgcactggcacctaaa\n-gtcgcttgcttgaattgcaacgaagtcgtatgtgtcttgctcgtaaactgtgcggaactt\n-ctggcgcacaaagtgtcctccctgctaatatggatccttggcatactaacatacgtctgc\n-cttaaagcgcgccttcggatacgcgagaagtccaacacgaggactcgagagagatacttc\n-cgcaaaaacgacagagaacacagatacaactactctgttatcgactccgacaatacaagc\n-atttcgtagaacacgagagggctaactacgcaaaagacgatctctttagcgtctggaaaa\n-cccgatacgaaatagcaagacaacgggagatcaataaggtacctaggaatacaaatagct\n-accttagtcgatttccatggagctcgccaggaaaacacagaataggaggaagacgcgctt\n-taactagtgccttctatactatcctattaggacacggatacctaaagtcctatctctatc\n-gctttggacacgtaacgacgccagactgcccttgcggacgacgagaaacagcagaacacc\n-tcgtatgtagctgccctatctacgatgtatttaggccactaccgctacgacaagcacaat\n-ctctactagaaatagtagaagataaggaactccggaaacacctcactacctttctctcgg\n-acacaaagattgcttctaggtcctggcacctagcaagaggcgaagacgagaccgtctagc\n-ctacactccttttacttttccttatttgtctttctttaaagtccttcgatactagctggc\n-tactatcctaggcacgggtctttccctaaggtcaagagatacgagagaacaacgattgta\n-catagatagactgctgtcgcgagacagccgtcctacatagtcatagactcctacaggacg\n-taaatGGaacaaacaaacaaacaaacaaatacgtctgccttatctaagacgcaatctagg\n-tcgagagccgatgtgccgcagctgcagttgtcggacaagaagagctcattcgcaaaaggg\n-taataggctttgccaagtgtagtgtcctttggctcgtacagccagagaacatcgagcgaa\n-gtacaatctttgcgagtgtgcacgttctaaacataggcataccatgcgtgcgctttgatc\n-ccctatttggtactgacatccggcgcgacgcatacgacatcccctgtgttcaccgtgact\n-gctttgttcccctcttgagattcgcttcggctcatactcctaggcgttaaggtttgcatt\n-ggcggtgcactcggagatgctcgtcgcggcgtcagtctgagccttacttttagctcatcc\n-gacttcttcagcacatttcggtccgtgatcgtccgctcttccagctggttaccgaagtac\n-atatgtcgaaagcactggtagacaaaaggcgtgacgatcgttcgcaactccttgtttggc\n-tgcgctgggatagctgtaagattatagggatcgacttcaccctagatcggttgtcggcac\n-aatccagactctttgtcatcgatatcccagcattctttccaaaggaagccgacatttgcg\n-gcaatggtcgtgcggaagtctttgagtttgcattcagctagccattagttaaagctagta\n-ttatcgccgtagagtctagttagctattggtaaaatcgtctgcggaaatgtccaagggta\n-acctgctggttgctgaggaggtagtcgacgaagtgcttcccgaactgtgctagctaaagg\n-aacggctcgtagaatcgacgatattccggtgcaggcgttcccagctcgtaccaatgacta\n-aacagagcggacgctttcgactacagcttcgattaaatgcagatgctactggcaaaatct\n-gtaaagtccaggtcgccgtacctactgatagccaagatctcgaactgcacgccctacatg\n-tagcgcttttcgttgcctgccgatagaatgccatcgaaacagaactctgcatagtttgat\n-tgccgcagtttctcaagagtgacgaggtccgatgcgcgtcgtccgtccgctatgtatacc\n-gagaattgatcgagtttgaaagtagcacattccggagtttcggtgctagcagacttcgca\n-gctgcgaagaagcctgcactcaagtctaggcttgcttcgacctcgtttacaggttgcaaa\n-ggaggtttgtatccgtagtaagcgcttctcggaaatgctggtcctacaatggagatgtgg\n-cttaagtagcgaagctgccgtcgtttcccggaacgagctgtggccccaggctctgctcta\n-gtagcaggctcgtcccctagttctgtttcggtcgctggaggagtgagtgcagtcctgagc\n-cttcgttgtctgggcgtgcgtagtgggccctagtccttaacttcccgatctccgactgtt\n-tggcttgtctgctcctcgcccaattctatcttatactaaaccgctctctgcactccatct\n-tcttcttgttgtttcgactcgcctcggtcctgctcagaagccgcaggactgattacaatc\n-gcattgcttagggaagctctagtgcgcaaaatgtctatctacaattgtccattctgaagc\n-cgcggcttcttggaaggcctcgaagtaggtcctaccacaatgttgtcctcgtcatcctga\n-atgacaatcgtgtcgccgctgatccgtctcttcatggttgccgtgctacttaatgccgtc\n-gtgtgcgaggtagtaatagggttaagaatgccgctgtcttgctacaaaggcgccatgttc\n-ttttcgttgctcgaagcagtccgtccgcggtaagtgtgccaaatcgcacaatgcaagtgc\n-tagagctgcaagtgaagtccaagagtgaatgcactaactatttaccttgcaagccgtgca\n-cgcagtgtaatgatctgccgaagcaaagaagaaatagcagaccaagatatccgcaaaaca\n-aatatccgtagaggtaaaaaggaatgcgcgcaacttgccagtaaaacgttgcttcgtgag\n-gtagttaatgaagtgtagtctggaagctttgaagtgcgaccaaggatgttctagccattg\n-acttttgaccgcgcctgcacctcaatgcccgtaatggccgccatcgcgaatggcatatgt\n-tagcgctgttaaattcaaatagtagaagtgagatggattatattcgagattacttatgta\n-cgcctacttgagggcggtggcatgtaacccgagtcttcgcttaagtgttgttacgaacgc\n-ttgaggtcctcctcgactgttccttgtccggctacggcatcgcgctgggcccaggcctct\n-cgtattcggggtttggcgtccctcgctcttttgtatgctcggagagggcggctcaaaagt\n-'..b'CAGCCAAGCAGCAGCCAAAGTACGACGCAC\n-AAACCAGGATGATTCACCATCAAAGCAAACAAATATGAGGTTCAACGAGAGGTGTGAGGT\n-ATAATGACTTCGAGCATGAGCCGGTGCTTGGCCCTTCTCGAGTATGCTCGTGCCATCTGC\n-TGTCCTTTTCGAAGATATTGCATGTGCATGAACATTTCTGGAGAAGGGCCTCGCTGAGAT\n-CACACGGCTCGAACTTGAACCAGATAATGCTGGCGATAAAGAATCATGCTCTTCCCCTAC\n-AGTCCAATCCCTACGAGCGAGGACTAACCCATCTAGGTATACACAACGGCAAAAGCGAAG\n-CGACCATGCCAGATCTCGACTCGAGAGATGTCGAGAAGAATGCCCTGGATTCACCTGAGA\n-TGCACGGTCCGGAGTCGGCCACATCCTCCACCGCCTCAGAAGGCCGCTCAAGGAACTTCC\n-TCAGCAGCGTCAAGCAGTCCGTCGTACACGACAACTTCGAGGCTCGCGGCGTCCAACGAG\n-TACTCCCAGCCGAGCGCAATCCGACATCCACATTTGGCTTTCTCCAAATCATGCTTATGT\n-GGATGAGCATCAACATGACCGCCGTCGTGATCGTCCTGGGCTTCCTCGGGCCCATCACTT\n-TCTCCTTATCCTTCAAAGATGCCTCTCTCCTTGCAGTCTTCGGCGCAATAGTTGGAGCGA\n-CGCCGGTCGCCTACATCGCCACTTTCGGCCCTCGCTCCGGCAACCGCACCATGATCCTCA\n-CCCGATACATCACCGGTTGGTGGCCATCCAAAGTCATCGTCATTCTCACACTCATCATCC\n-TCATGGGCTACGTCCTCCTCGACGCCGTTATTGGCGGTCAGATCCTCTCAGCCGTCAGTC\n-CCAACGCTTCCCTCAGCGTCATAGTCGGCATCGTCATCGTCTGCATCCTCACCTGGATCG\n-TGACCGCATTCGGCTATTGTGTCTTCCATCACTTCGAGCGCTACGCCTGGATCCCCTCCC\n-TCATCGTCATTTGTCTCCTCATCGGCGTCTCCGCTCCAAAATGGAATCTCGAACCAGGTC\n-CCGCTCTCCCACCTCGCACCCTCGCCGGCAACCGCCTCTCCTTCTTCTCTCTTTGTCTCG\n-CCGCCGAAATCACCTACGCCGAATCGGGAGCCGACATGTTTGTCTACTATCCATCCACCA\n-CTTCCCGCACAAAAGTCTTTCTCTCCACCCTCGCTGGTCTCACCCTCTCCTCCGCCATCG\n-CCCTCATCACCGGTATTGGCCTCGGCTCCGGCACTCTCACCGATCCAGCCTGGTCCTCCG\n-CCTACTCCGTCTCCGCAGGTGCCCTCATCGTTGAAGCATTCCGTCCACTCGGTGGATTCG\n-GCTCATTCTGCAGCGTTCTCGTTGCACTGGGTATAGTCGCAAATATGGTCCTGCCGACCT\n-ACGCTTCAGGAGTGGACTTCCAAGCGTTCGGCCGATGGTTCGAAAGGGTCCCGCGGATCG\n-TGTGGAATACCGTTGCGCTGGTCGTACCGATGATTGGAGCAATCGCAGGACGAGAACACC\n-TGGCGGAGATCTTCTCCAACTTCCTGGCATTGATGGGTTATTGGGTGTCTATCTGGATTG\n-CGATCGTGGTGGAAGAGCACATCTTGTTCCGAAAGATGGGAGGCAAGGGTTGGAAGTGGG\n-AGGACTGGAATGACAGGACGAAGCTCCCTATCGGTATTGCGGCGGGCGTTGCGTTCCTTG\n-TGGGATGGGTTGGAGCGATTATGGGTATGTCGCAGGTCTGGTATGTGGGACCGTTGGCGA\n-AGCTGGTCAGTGAGCAGGGAGCGGATATCGGGAATTATGTTGGGTTTTCGTGGGCGTTGG\n-TGGTGTATCCGCCTTTGAGGTGGGTGGAGCTGAGGTGGGTTGGGAGATAGGAGGGCAGAT\n-GGAGGATGGAGGAAGTCGGTGGACAGATCAAGGCGGAGAATCGGAGGTTGTGAAGCCCTC\n-GAGTTGTGGCTCGGGATGTGCCTGCGCTGTTTATCTTTGCGGCACTCAACTCCGCCAACA\n-GCATGCATTCGTGCGAGCAACGCAGACAAATTCAGCGTATCCTCTCGAGCATTGATATGG\n-CAAGCCCGAATACGCTCAACTCTGCGCCCTTCTCCGTTCATTCAACAGCATATACTCATA\n-CCGACATCAATATTCGTTATCATTATTTGCACAACTAGCGGTGAATCGCGATGAAGCCCG\n-ACTTACCTTAGTCATGCACTGCATCCGACATCGGGACGCGTATCGCCCGCATTCTTGGCA\n-CCTCCCCGGGCGCAAAATCCTGTTATCTTCCCGGCTGGCTCCCTCCTTCTTTTCATATGC\n-ACGCGTAATCCTCACCGTCTCTCCCTTTCACATTCACGCACCAGTTCACAATAACAATAT\n-TCACGCTTGACTTCACCTCACTTCACTGCCACCCCTCCCTACCTCACTCTTTCCCACTGC\n-TGCGCAGTCATGCCTCGCCCTCCAGACCACTACACCCACGCCCAATTCGAGCCCGTCGAG\n-TCGGACCACGCCGGCGAAACGGTCCAATGTCGCCACTGCCGCAACTGGACGGGTTCCATC\n-AAGACGCTTAATCGGAAAAAAGCTCATCTTCTCACGTGCACGCAGTATGCGCAGTGGCGG\n-GCGGCGGGGAATGGGCAGGATTTGGCGCCGCCGAATAAGTATCATAAGAGGGATAGTTCG\n-GTTATGGGTGGTGGGTGGGAGGGGCAGGGGGATGGGTCAGTGATCTTCTTTTGATGTTGT\n-GGTGTTTTGTGGTGGCTTGAAGATGGAATTGCGATGATTTGGGTTCTTTGTGATGTTGGT\n-GGAATGCTAACGGTGTTATTGCAGGAATACCTCTGGCTTCAATATGTCGCCGTTCAATGA\n-TACCCCGACGGTGGCTCGTGGCCGCAATCTTGATCTGACCAAGGTAGACATTGACAAGAT\n-GTTCCAATTCGCTGCAGTATACTGATCATGTACAGTACTTCTCCGAATTCTGGGACGACA\n-CCGCTTCGAACAAGGTCAGTGACTATCTACAGGATTTTACAGGCAATCTGTCTATTGTCA\n-CTTTCGTGATCCTCTGCATCTTCAGATCCAGCGCCACAAGTACTTACAAGTATCTACCAG\n-TGCATGCGAGTACGCTGCCTCTCCTGCGGCTTCGTCCGGGCAAAGAACACCACCCGCCAA\n-GTCGAACATCTTGCCAGCTGCGCCTCGTTCCTCAACAGCACCGAAGGTCAAGCCGCTGTC\n-GCGAACGGCGAACTCGAAATGACACCTGCCGCACCTCGCCAGTCTTTCGGAGGCGGGAAT\n-GACATCTGGCGTGGCGGTGCACCAAACCCGAATCTGCAAGTCAGCCAGACGCCAACTTCG\n-ACCAGCCGTGGTGGAGGAAGAGCCTATCCGATGCCGCCTCCTCCCAAAGCACCCTCCCTC\n-GTATCTCACCTCCTCAACAAGTTCCAGGAAAAGTTCAATGTTGCGACTCAACAGTCTTTC\n-CTCTCTCACGCCGGCTGCGGTACTCTGTCCCACGCAGCTCTCTGCTCCTGGCTCACACAG\n-CATGGCCACATTTCTCGAGCTATGATTGCCGCCATTGGATCACTCATCGCCAAAGTGTTC\n-CTGCCAGATGCCGCCAATACTCGCATTGCTACGCCATACCGTGCTCTGGACCTGCTCATC\n-TCCACGATCAGCAATCTTCGTAAAGAGATCGACTTCATCGAGAATACTAAGCGGAAGTAT\n-CGCTTGGACGCTGCGAGTGAGCCGCCGTCGCCGATGACGAAGGCATACGTCGATCTCTTG\n-GCGAGTGCTTCTGAGCCGAGAGCAGATCTGCTGGAGGGAATGGTAGCGCTGTGGGCGACC\n-GAGCATGTATGTTGACCACCTTTTCCGTTTCTGTGTTCGATGTCACTAACTCTATACCAG\n' |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a test-data/seq-mdust.fsa --- a/test-data/seq-mdust.fsa Mon Oct 05 11:05:21 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| b'@@ -1,5000 +0,0 @@\n->seqmdust\n-ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa\n-ccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaaccctaa\n-ccctcaccctcaccctCGgtcgtacggcgtgacaatgtctccagaatcgatttggtcttg\n-acgaaagcagcgcacatagcacttccggatgattttgtcgcatgctttgtcaaacacgac\n-gtccgtaagtactagctcgttcggcctagctttcgcgcccgtctgctgctcgctcttccg\n-caagaattgacgcagaacgacgcgccgcttctgggtatcgaactcgataatttgggctgg\n-ctggagccggtcctcgtcaaggtcgtcattccattcgcggacgaggacggtgtcaccaat\n-tgcatatttgctccggcactcgtcgaatataggaacgtcatgcttgcactggcacctaaa\n-gtcgcttgcttgaattgcaacgaagtcgtatgtgtcttgctcgtaaactgtgcggaactt\n-ctggcgcacaaagtgtcctccctgctaatatggatccttggcatactaacatacgtctgc\n-cttaaagcgcgccttcggatacgcgagaagtccaacacgaggactcgagagagatacttc\n-cgcaaaaacgacagagaacacagatacaactactctgttatcgactccgacaatacaagc\n-atttcgtagaacacgagagggctaactacgcaaaagacgatctctttagcgtctggaaaa\n-cccgatacgaaatagcaagacaacgggagatcaataaggtacctaggaatacaaatagct\n-accttagtcgatttccatggagctcgccaggaaaacacagaataggaggaagacgcgctt\n-taactagtgccttctatactatcctattaggacacggatacctaaagtcctatctctatc\n-gctttggacacgtaacgacgccagactgcccttgcggacgacgagaaacagcagaacacc\n-tcgtatgtagctgccctatctacgatgtatttaggccactaccgctacgacaagcacaat\n-ctctactagaaatagtagaagataaggaactccggaaacacctcactacctttctctcgg\n-acacaaagattgcttctaggtcctggcacctagcaagaggcgaagacgagaccgtctagc\n-ctacactccttttacttttccttatttgtctttctttaaagtccttcgatactagctggc\n-tactatcctaggcacgggtctttccctaaggtcaagagatacgagagaacaacgattgta\n-catagatagactgctgtcgcgagacagccgtcctacatagtcatagactcctacaggacg\n-taaatGGaacaaacaaacaaacaaacaaatacgtctgccttatctaagacgcaatctagg\n-tcgagagccgatgtgccgcagctgcagttgtcggacaagaagagctcattcgcaaaaggg\n-taataggctttgccaagtgtagtgtcctttggctcgtacagccagagaacatcgagcgaa\n-gtacaatctttgcgagtgtgcacgttctaaacataggcataccatgcgtgcgctttgatc\n-ccctatttggtactgacatccggcgcgacgcatacgacatcccctgtgttcaccgtgact\n-gctttgttcccctcttgagattcgcttcggctcatactcctaggcgttaaggtttgcatt\n-ggcggtgcactcggagatgctcgtcgcggcgtcagtctgagccttacttttagctcatcc\n-gacttcttcagcacatttcggtccgtgatcgtccgctcttccagctggttaccgaagtac\n-atatgtcgaaagcactggtagacaaaaggcgtgacgatcgttcgcaactccttgtttggc\n-tgcgctgggatagctgtaagattatagggatcgacttcaccctagatcggttgtcggcac\n-aatccagactctttgtcatcgatatcccagcattctttccaaaggaagccgacatttgcg\n-gcaatggtcgtgcggaagtctttgagtttgcattcagctagccattagttaaagctagta\n-ttatcgccgtagagtctagttagctattggtaaaatcgtctgcggaaatgtccaagggta\n-acctgctggttgctgaggaggtagtcgacgaagtgcttcccgaactgtgctagctaaagg\n-aacggctcgtagaatcgacgatattccggtgcaggcgttcccagctcgtaccaatgacta\n-aacagagcggacgctttcgactacagcttcgattaaatgcagatgctactggcaaaatct\n-gtaaagtccaggtcgccgtacctactgatagccaagatctcgaactgcacgccctacatg\n-tagcgcttttcgttgcctgccgatagaatgccatcgaaacagaactctgcatagtttgat\n-tgccgcagtttctcaagagtgacgaggtccgatgcgcgtcgtccgtccgctatgtatacc\n-gagaattgatcgagtttgaaagtagcacattccggagtttcggtgctagcagacttcgca\n-gctgcgaagaagcctgcactcaagtctaggcttgcttcgacctcgtttacaggttgcaaa\n-ggaggtttgtatccgtagtaagcgcttctcggaaatgctggtcctacaatggagatgtgg\n-cttaagtagcgaagctgccgtcgtttcccggaacgagctgtggccccaggctctgctcta\n-gtagcaggctcgtcccctagttctgtttcggtcgctggaggagtgagtgcagtcctgagc\n-cttcgttgtctgggcgtgcgtagtgggccctagtccttaacttcccgatctccgactgtt\n-tggcttgtctgctcctcgcccaattctatcttatactaaaccgctctctgcactccatct\n-tcttcttgttgtttcgactcgcctcggtcctgctcagaagccgcaggactgattacaatc\n-gcattgcttagggaagctctagtgcgcaaaatgtctatctacaattgtccattctgaagc\n-cgcggcttcttggaaggcctcgaagtaggtcctaccacaatgttgtcctcgtcatcctga\n-atgacaatcgtgtcgccgctgatccgtctcttcatggttgccgtgctacttaatgccgtc\n-gtgtgcgaggtagtaatagggttaagaatgccgctgtcttgctacaaaggcgccatgttc\n-ttttcgttgctcgaagcagtccgtccgcggtaagtgtgccaaatcgcacaatgcaagtgc\n-tagagctgcaagtgaagtccaagagtgaatgcactaactatttaccttgcaagccgtgca\n-cgcagtgtaatgatctgccgaagcaaagaagaaatagcagaccaagatatccgcaaaaca\n-aatatccgtagaggtaaaaaggaatgcgcgcaacttgccagtaaaacgttgcttcgtgag\n-gtagttaatgaagtgtagtctggaagctttgaagtgcgaccaaggatgttctagccattg\n-acttttgaccgcgcctgcacctcaatgcccgtaatggccgccatcgcgaatggcatatgt\n-tagcgctgttaaattcaaatagtagaagtgagatggattatattcgagattacttatgta\n-cgcctacttgagggcggtggcatgtaacccgagtcttcgcttaagtgttgttacgaacgc\n-ttgaggtcctcctcgactgttccttgtccggctacggcatcgcgctgggcccaggcctct\n-cgtattcggggtttggcgtccctcgctcttttgtatgctcggagagggcggctcaaaagt\n-'..b'CAGCCAAGCAGCAGCCAAAGTACGACGCAC\n-AAACCAGGATGATTCACCATCAAAGCAAACAAATATGAGGTTCAACGAGAGGTGTGAGGT\n-ATAATGACTTCGAGCATGAGCCGGTGCTTGGCCCTTCTCGAGTATGCTCGTGCCATCTGC\n-TGTCCTTTTCGAAGATATTGCATGTGCATGAACATTTCTGGAGAAGGGCCTCGCTGAGAT\n-CACACGGCTCGAACTTGAACCAGATAATGCTGGCGATAAAGAATCATGCTCTTCCCCTAC\n-AGTCCAATCCCTACGAGCGAGGACTAACCCATCTAGGTATACACAACGGCAAAAGCGAAG\n-CGACCATGCCAGATCTCGACTCGAGAGATGTCGAGAAGAATGCCCTGGATTCACCTGAGA\n-TGCACGGTCCGGAGTCGGCCACATCCTCCACCGCCTCAGAAGGCCGCTCAAGGAACTTCC\n-TCAGCAGCGTCAAGCAGTCCGTCGTACACGACAACTTCGAGGCTCGCGGCGTCCAACGAG\n-TACTCCCAGCCGAGCGCAATCCGACATCCACATTTGGCTTTCTCCAAATCATGCTTATGT\n-GGATGAGCATCAACATGACCGCCGTCGTGATCGTCCTGGGCTTCCTCGGGCCCATCACTT\n-TCTCCTTATCCTTCAAAGATGCCTCTCTCCTTGCAGTCTTCGGCGCAATAGTTGGAGCGA\n-CGCCGGTCGCCTACATCGCCACTTTCGGCCCTCGCTCCGGCAACCGCACCATGATCCTCA\n-CCCGATACATCACCGGTTGGTGGCCATCCAAAGTCATCGTCATTCTCACACTCATCATCC\n-TCATGGGCTACGTCCTCCTCGACGCCGTTATTGGCGGTCAGATCCTCTCAGCCGTCAGTC\n-CCAACGCTTCCCTCAGCGTCATAGTCGGCATCGTCATCGTCTGCATCCTCACCTGGATCG\n-TGACCGCATTCGGCTATTGTGTCTTCCATCACTTCGAGCGCTACGCCTGGATCCCCTCCC\n-TCATCGTCATTTGTCTCCTCATCGGCGTCTCCGCTCCAAAATGGAATCTCGAACCAGGTC\n-CCGCTCTCCCACCTCGCACCCTCGCCGGCAACCGCCTCTCCTTCTTCTCTCTTTGTCTCG\n-CCGCCGAAATCACCTACGCCGAATCGGGAGCCGACATGTTTGTCTACTATCCATCCACCA\n-CTTCCCGCACAAAAGTCTTTCTCTCCACCCTCGCTGGTCTCACCCTCTCCTCCGCCATCG\n-CCCTCATCACCGGTATTGGCCTCGGCTCCGGCACTCTCACCGATCCAGCCTGGTCCTCCG\n-CCTACTCCGTCTCCGCAGGTGCCCTCATCGTTGAAGCATTCCGTCCACTCGGTGGATTCG\n-GCTCATTCTGCAGCGTTCTCGTTGCACTGGGTATAGTCGCAAATATGGTCCTGCCGACCT\n-ACGCTTCAGGAGTGGACTTCCAAGCGTTCGGCCGATGGTTCGAAAGGGTCCCGCGGATCG\n-TGTGGAATACCGTTGCGCTGGTCGTACCGATGATTGGAGCAATCGCAGGACGAGAACACC\n-TGGCGGAGATCTTCTCCAACTTCCTGGCATTGATGGGTTATTGGGTGTCTATCTGGATTG\n-CGATCGTGGTGGAAGAGCACATCTTGTTCCGAAAGATGGGAGGCAAGGGTTGGAAGTGGG\n-AGGACTGGAATGACAGGACGAAGCTCCCTATCGGTATTGCGGCGGGCGTTGCGTTCCTTG\n-TGGGATGGGTTGGAGCGATTATGGGTATGTCGCAGGTCTGGTATGTGGGACCGTTGGCGA\n-AGCTGGTCAGTGAGCAGGGAGCGGATATCGGGAATTATGTTGGGTTTTCGTGGGCGTTGG\n-TGGTGTATCCGCCTTTGAGGTGGGTGGAGCTGAGGTGGGTTGGGAGATAGGAGGGCAGAT\n-GGAGGATGGAGGAAGTCGGTGGACAGATCAAGGCGGAGAATCGGAGGTTGTGAAGCCCTC\n-GAGTTGTGGCTCGGGATGTGCCTGCGCTGTTTATCTTTGCGGCACTCAACTCCGCCAACA\n-GCATGCATTCGTGCGAGCAACGCAGACAAATTCAGCGTATCCTCTCGAGCATTGATATGG\n-CAAGCCCGAATACGCTCAACTCTGCGCCCTTCTCCGTTCATTCAACAGCATATACTCATA\n-CCGACATCAATATTCGTTATCATTATTTGCACAACTAGCGGTGAATCGCGATGAAGCCCG\n-ACTTACCTTAGTCATGCACTGCATCCGACATCGGGACGCGTATCGCCCGCATTCTTGGCA\n-CCTCCCCGGGCGCAAAATCCTGTTATCTTCCCGGCTGGCTCCCTCCTTCTTTTCATATGC\n-ACGCGTAATCCTCACCGTCTCTCCCTTTCACATTCACGCACCAGTTCACAATAACAATAT\n-TCACGCTTGACTTCACCTCACTTCACTGCCACCCCTCCCTACCTCACTCTTTCCCACTGC\n-TGCGCAGTCATGCCTCGCCCTCCAGACCACTACACCCACGCCCAATTCGAGCCCGTCGAG\n-TCGGACCACGCCGGCGAAACGGTCCAATGTCGCCACTGCCGCAACTGGACGGGTTCCATC\n-AAGACGCTTAATCGGAAAAAAGCTCATCTTCTCACGTGCACGCAGTATGCGCAGTGGCGG\n-GCGGCGGGGAATGGGCAGGATTTGGCGCCGCCGAATAAGTATCATAAGAGGGATAGTTCG\n-GTTATGGGTGGTGGGTGGGAGGGGCAGGGGGATGGGTCAGTGATCTTCTTTTGATGTTGT\n-GGTGTTTTGTGGTGGCTTGAAGATGGAATTGCGATGATTTGGGTTCTTTGTGATGTTGGT\n-GGAATGCTAACGGTGTTATTGCAGGAATACCTCTGGCTTCAATATGTCGCCGTTCAATGA\n-TACCCCGACGGTGGCTCGTGGCCGCAATCTTGATCTGACCAAGGTAGACATTGACAAGAT\n-GTTCCAATTCGCTGCAGTATACTGATCATGTACAGTACTTCTCCGAATTCTGGGACGACA\n-CCGCTTCGAACAAGGTCAGTGACTATCTACAGGATTTTACAGGCAATCTGTCTATTGTCA\n-CTTTCGTGATCCTCTGCATCTTCAGATCCAGCGCCACAAGTACTTACAAGTATCTACCAG\n-TGCATGCGAGTACGCTGCCTCTCCTGCGGCTTCGTCCGGGCAAAGAACACCACCCGCCAA\n-GTCGAACATCTTGCCAGCTGCGCCTCGTTCCTCAACAGCACCGAAGGTCAAGCCGCTGTC\n-GCGAACGGCGAACTCGAAATGACACCTGCCGCACCTCGCCAGTCTTTCGGAGGCGGGAAT\n-GACATCTGGCGTGGCGGTGCACCAAACCCGAATCTGCAAGTCAGCCAGACGCCAACTTCG\n-ACCAGCCGTGGTGGAGGAAGAGCCTATCCGATGCCGCCTCCTCCCAAAGCACCCTCCCTC\n-GTATCTCACCTCCTCAACAAGTTCCAGGAAAAGTTCAATGTTGCGACTCAACAGTCTTTC\n-CTCTCTCACGCCGGCTGCGGTACTCTGTCCCACGCAGCTCTCTGCTCCTGGCTCACACAG\n-CATGGCCACATTTCTCGAGCTATGATTGCCGCCATTGGATCACTCATCGCCAAAGTGTTC\n-CTGCCAGATGCCGCCAATACTCGCATTGCTACGCCATACCGTGCTCTGGACCTGCTCATC\n-TCCACGATCAGCAATCTTCGTAAAGAGATCGACTTCATCGAGAATACTAAGCGGAAGTAT\n-CGCTTGGACGCTGCGAGTGAGCCGCCGTCGCCGATGACGAAGGCATACGTCGATCTCTTG\n-GCGAGTGCTTCTGAGCCGAGAGCAGATCTGCTGGAGGGAATGGTAGCGCTGTGGGCGACC\n-GAGCATGTATGTTGACCACCTTTTCCGTTTCTGTGTTCGATGTCACTAACTCTATACCAG\n' |
| b |
| diff -r cc6db1ee2d48 -r 034d5b66e97a tool_dependencies.xml --- a/tool_dependencies.xml Mon Oct 05 11:05:21 2015 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
| b |
| @@ -1,18 +0,0 @@ -<?xml version="1.0"?> -<tool_dependency> - <package name="mdust" version="1.0"> - <install version="1.0"> - <actions> - <action type="download_by_url">ftp://occams.dfci.harvard.edu/pub/bio/tgi/software/seqclean/mdust.tar.gz</action> - <action type="shell_command">make</action> - <action type="move_file"> - <source>mdust</source> - <destination>$INSTALL_DIR</destination> - </action> - <action type="set_environment"> - <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> - </action> - </actions> - </install> - </package> -</tool_dependency> |