# HG changeset patch
# User peterjc
# Date 1366821797 14400
# Node ID 4266cccbb45aa3360b83c159ac111f3286f0d5e3
# Parent 4d3f94dfb857b5651db2176f28c6cda964308110
Uploaded v0.0.7 take 2, fixed path in installation
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/mira_3_4/mira.py
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.py Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,124 @@
+#!/usr/bin/env python
+"""A simple wrapper script to call MIRA and collect its output.
+"""
+import os
+import sys
+import subprocess
+import shutil
+import time
+
+WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
+
+def stop_err(msg, err=1):
+ sys.stderr.write(msg+"\n")
+ sys.exit(err)
+
+
+def get_version():
+ """Run MIRA to find its version number"""
+ # At the commend line I would use: mira -v | head -n 1
+ # however there is some pipe error when doing that here.
+ try:
+ child = subprocess.Popen(["mira", "-v"],
+ stdout=subprocess.PIPE,
+ stderr=subprocess.STDOUT)
+ except Exception, err:
+ sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
+ sys.exit(1)
+ ver, tmp = child.communicate()
+ del child
+ return ver.split("\n", 1)[0]
+
+
+mira_ver = get_version()
+if "V3.4." not in mira_ver:
+ stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
+if "-v" in sys.argv:
+ print "MIRA wrapper version %s," % WRAPPER_VER
+ print mira_ver
+ sys.exit(0)
+
+
+def collect_output(temp, name):
+ n3 = (temp, name, name, name)
+ f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
+ if not os.path.isdir(f):
+ stop_err("Missing output folder")
+ if not os.listdir(f):
+ stop_err("Empty output folder")
+ missing = []
+ for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
+ ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
+ ("%s/%s_out.wig" % (f, name), out_wig),
+ ("%s/%s_out.caf" % (f, name), out_caf),
+ ("%s/%s_out.ace" % (f, name), out_ace)]:
+ if not os.path.isfile(old):
+ missing.append(os.path.splitext(old)[-1])
+ else:
+ shutil.move(old, new)
+ if missing:
+ stop_err("Missing output files: %s" % ", ".join(missing))
+
+def clean_up(temp, name):
+ folder = "%s/%s_assembly" % (temp, name)
+ if os.path.isdir(folder):
+ shutil.rmtree(folder)
+
+#TODO - Run MIRA in /tmp or a configurable directory?
+#Currently Galaxy puts us somewhere safe like:
+#/opt/galaxy-dist/database/job_working_directory/846/
+temp = "."
+name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
+
+start_time = time.time()
+cmd_list =sys.argv[8:]
+cmd = " ".join(cmd_list)
+
+assert os.path.isdir(temp)
+d = "%s_assembly" % name
+assert not os.path.isdir(d), "Path %s already exists" % d
+try:
+ #Check path access
+ os.mkdir(d)
+except Exception, err:
+ sys.stderr.write("Error making directory %s\n%s" % (d, err))
+ sys.exit(1)
+
+#print os.path.abspath(".")
+#print cmd
+
+handle = open(out_log, "w")
+try:
+ #Run MIRA
+ child = subprocess.Popen(cmd_list,
+ stdout=handle,
+ stderr=subprocess.STDOUT)
+except Exception, err:
+ sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+ #TODO - call clean up?
+ handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
+ handle.close()
+ sys.exit(1)
+#Use .communicate as can get deadlocks with .wait(),
+stdout, stderr = child.communicate()
+assert not stdout and not stderr #Should be empty as sent to handle
+run_time = time.time() - start_time
+return_code = child.returncode
+handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
+print "MIRA took %0.2f minutes" % (run_time / 60.0)
+if return_code:
+ handle.write("Return error code %i from command:\n" % return_code)
+ handle.write(cmd + "\n")
+ handle.close()
+ clean_up(temp, name)
+ stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+ return_code)
+handle.close()
+
+#print "Collecting output..."
+collect_output(temp, name)
+
+#print "Cleaning up..."
+clean_up(temp, name)
+
+print "Done"
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/mira_3_4/mira.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.txt Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,104 @@
+Galaxy tool to wrap the MIRA sequence assembly program (v3.4)
+=============================================================
+
+This tool is copyright 2011-2013 by Peter Cock, The James Hutton Institute
+(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
+See the licence text below.
+
+This tool is a short Python script (to collect the MIRA output and move it
+to where Galaxy expects the files, and convert MIRA's TCS file into a tab
+separated file for use in Galaxy).
+
+
+Automated Installation
+======================
+
+This should be straightforward, Galaxy should automatically download and
+install the precompiled binary for MIRA v3.4.0 for the Galaxy wrapper,
+and run any tests.
+
+
+Manual Installation
+===================
+
+There are just two Galaxy files to install:
+
+* mira.py (the Python script)
+* mira.xml (the Galaxy tool definition)
+
+The suggested location is a new tools/mira_3_4 folder. You will also need to
+modify the tools_conf.xml file to tell Galaxy to offer the tool, and also do
+this to tools_conf.xml.sample in order to run any tests:
+
+
+
+You will also need to install MIRA, we used version 3.4.1.1. See:
+
+http://chevreux.org/projects_mira.html
+http://sourceforge.net/projects/mira-assembler/
+
+WARNING: This tool was developed to construct viral genome assembly and
+mapping pipelines, for which the run time and memory requirements are
+negligible. For larger tasks, be aware that MIRA can require vast amounts
+of RAM and run-times of over a week are possible. This tool wrapper makes
+no attempt to spot and reject such large jobs.
+
+
+History
+=======
+
+v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
+v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
+v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
+ (some other switches changed, e.g. -OUT rrol to rrot, which
+ means the wrapper no longer works with MIRA 3.2.x)
+ - The contig summary file (TCS file) was removed in MIRA 3.4
+ - Report all missing output files (not just first missing one)
+v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
+v0.0.5 - Implement the tag to record the wrapper
+ version and the MIRA version being used.
+ - Check using MIRA 3.4 (later versions have a different API)
+v0.0.6 - Tell MIRA to use /tmp for temporary files
+ - Tell MIRA to ignore long read names (otherwise it aborts)
+v0.0.7 - Automated installation of the 64 bit Linux MIRA binary.
+
+
+Developers
+==========
+
+This script and related tools are being developed on the following hg branch:
+http://bitbucket.org/peterjc/galaxy-central/src/tools
+
+For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
+the following command from the Galaxy root folder:
+
+tar -czf mira_wrapper.tar.gz tools/mira_3_4/mira.*
+
+Check this worked:
+
+$ tar -tzf mira_wrapper.tar.gz
+tools/mira_3_4/mira.py
+tools/mira_3_4/mira.txt
+tools/mira_3_4/mira.xml
+
+
+Licence (MIT/BSD style)
+=======================
+
+Permission to use, copy, modify, and distribute this software and its
+documentation with or without modifications and for any purpose and
+without fee is hereby granted, provided that any copyright notices
+appear in all copies and that both those copyright notices and this
+permission notice appear in supporting documentation, and that the
+names of the contributors or copyright holders not be used in
+advertising or publicity pertaining to distribution of the software
+without specific prior permission.
+
+THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
+WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
+WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
+CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
+OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
+OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
+OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
+OR PERFORMANCE OF THIS SOFTWARE.
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/mira_3_4/mira.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mira_3_4/mira.xml Wed Apr 24 12:43:17 2013 -0400
@@ -0,0 +1,155 @@
+
+ Takes Sanger, Roche, Illumina, and Ion Torrent data
+ mira.py -v
+ mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
+##Give the wrapper script list of output filenames, then the mira command...
+mira --job=$job_method,$job_type,$job_quality
+
+##Input files
+#if $condBackbone.use == "true":
+ ## Can this be linked to job_method as well? If mapping we need the backbone...
+ -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
+#end if
+#if $condSanger.use == "true":
+ SANGER_SETTINGS
+ ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
+ ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+ -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
+#end if
+#if $condRoche.use == "true":
+ 454_SETTINGS
+ ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
+ ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+ -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
+#end if
+#if $condIllumina.use == "true":
+ SOLEXA_SETTINGS
+ ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
+ -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
+ ##TODO - Look at -LR FASTQ qual offset (fqqo)
+#end if
+#if $condIonTorrent.use == "true":
+ IONTOR_SETTINGS
+ ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
+ ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
+ -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
+#end if
+
+##Output files
+COMMON_SETTINGS
+
+##ignore warnings about long read names
+-MI:somrnl=0
+
+##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
+##Explicitly disable formats we won't use like MAF (reduce IO)
+-OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
+
+##remove_rollover_tmps, remove_tmp_directory
+-OUT:rrot=1:rtd=1
+
+##put mira temp directory on local storage
+-DI:trt=/tmp
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
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+
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+
+
+
+ Bio
+ mira
+
+
+
+**What it does**
+
+Runs MIRA v3.4, collects the output, and throws away all the temporary files.
+
+**Citation**
+
+If you use this tool in scientific work leading to a publication, please cite:
+
+Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
+
+
+
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/sr_assembly/mira.py
--- a/tools/sr_assembly/mira.py Thu Feb 14 06:26:32 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-#!/usr/bin/env python
-"""A simple wrapper script to call MIRA and collect its output.
-"""
-import os
-import sys
-import subprocess
-import shutil
-import time
-
-WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
-
-def stop_err(msg, err=1):
- sys.stderr.write(msg+"\n")
- sys.exit(err)
-
-
-def get_version():
- """Run MIRA to find its version number"""
- # At the commend line I would use: mira -v | head -n 1
- # however there is some pipe error when doing that here.
- try:
- child = subprocess.Popen(["mira", "-v"],
- stdout=subprocess.PIPE,
- stderr=subprocess.STDOUT)
- except Exception, err:
- sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (" ".join(cmd), err))
- sys.exit(1)
- ver, tmp = child.communicate()
- del child
- return ver.split("\n", 1)[0]
-
-
-mira_ver = get_version()
-if "V3.4." not in mira_ver:
- stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
-if "-v" in sys.argv:
- print "MIRA wrapper version %s," % WRAPPER_VER
- print mira_ver
- sys.exit(0)
-
-
-def collect_output(temp, name):
- n3 = (temp, name, name, name)
- f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
- if not os.path.isdir(f):
- stop_err("Missing output folder")
- if not os.listdir(f):
- stop_err("Empty output folder")
- missing = []
- for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
- ("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
- ("%s/%s_out.wig" % (f, name), out_wig),
- ("%s/%s_out.caf" % (f, name), out_caf),
- ("%s/%s_out.ace" % (f, name), out_ace)]:
- if not os.path.isfile(old):
- missing.append(os.path.splitext(old)[-1])
- else:
- shutil.move(old, new)
- if missing:
- stop_err("Missing output files: %s" % ", ".join(missing))
-
-def clean_up(temp, name):
- folder = "%s/%s_assembly" % (temp, name)
- if os.path.isdir(folder):
- shutil.rmtree(folder)
-
-#TODO - Run MIRA in /tmp or a configurable directory?
-#Currently Galaxy puts us somewhere safe like:
-#/opt/galaxy-dist/database/job_working_directory/846/
-temp = "."
-name, out_fasta, out_qual, out_ace, out_caf, out_wig, out_log = sys.argv[1:8]
-
-start_time = time.time()
-cmd_list =sys.argv[8:]
-cmd = " ".join(cmd_list)
-
-assert os.path.isdir(temp)
-d = "%s_assembly" % name
-assert not os.path.isdir(d), "Path %s already exists" % d
-try:
- #Check path access
- os.mkdir(d)
-except Exception, err:
- sys.stderr.write("Error making directory %s\n%s" % (d, err))
- sys.exit(1)
-
-#print os.path.abspath(".")
-#print cmd
-
-handle = open(out_log, "w")
-try:
- #Run MIRA
- child = subprocess.Popen(cmd_list,
- stdout=handle,
- stderr=subprocess.STDOUT)
-except Exception, err:
- sys.stderr.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
- #TODO - call clean up?
- handle.write("Error invoking command:\n%s\n\n%s\n" % (cmd, err))
- handle.close()
- sys.exit(1)
-#Use .communicate as can get deadlocks with .wait(),
-stdout, stderr = child.communicate()
-assert not stdout and not stderr #Should be empty as sent to handle
-run_time = time.time() - start_time
-return_code = child.returncode
-handle.write("\n\nMIRA took %0.2f minutes\n" % (run_time / 60.0))
-print "MIRA took %0.2f minutes" % (run_time / 60.0)
-if return_code:
- handle.write("Return error code %i from command:\n" % return_code)
- handle.write(cmd + "\n")
- handle.close()
- clean_up(temp, name)
- stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
- return_code)
-handle.close()
-
-#print "Collecting output..."
-collect_output(temp, name)
-
-#print "Cleaning up..."
-clean_up(temp, name)
-
-print "Done"
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/sr_assembly/mira.txt
--- a/tools/sr_assembly/mira.txt Thu Feb 14 06:26:32 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,89 +0,0 @@
-Galaxy tool to wrap the MIRA sequence assembly program
-======================================================
-
-This tool is copyright 2011 by Peter Cock, The James Hutton Institute
-(formerly SCRI, Scottish Crop Research Institute), UK. All rights reserved.
-See the licence text below.
-
-This tool is a short Python script (to collect the MIRA output and move it
-to where Galaxy expects the files, and convert MIRA's TCS file into a tab
-separated file for use in Galaxy). There are just two files to install:
-
-* mira.py (the Python script)
-* mira.xml (the Galaxy tool definition)
-
-The suggested location is the tools/sr_assembly folder. You will also need to
-modify the tools_conf.xml file to tell Galaxy to offer the tool and also do
-this to tools_conf.xml.sample in order to run any tests:
-
-
-
-You will also need to install MIRA, we used version 3.4.0. See:
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-
-WARNING: This tool was developed to construct viral genome assembly and
-mapping pipelines, for which the run time and memory requirements are
-negligible. For larger tasks, be aware that MIRA can require vast amounts
-of RAM and run-times of over a week are possible. This tool wrapper makes
-no attempt to spot and reject such large jobs.
-
-
-History
-=======
-
-v0.0.1 - Initial version (working prototype, using MIRA 3.2.1)
-v0.0.2 - Improve capture of stdout/stderr (should see it as it runs)
-v0.0.3 - Support Ion Torrent reads, now requires MIRA 3.4.0 or later
- (some other switches changed, e.g. -OUT rrol to rrot, which
- means the wrapper no longer works with MIRA 3.2.x)
- - The contig summary file (TCS file) was removed in MIRA 3.4
- - Report all missing output files (not just first missing one)
-v0.0.4 - Fix problem with backbone arguments inroduced in v0.0.3
-v0.0.5 - Implement the tag to record the wrapper
- version and the MIRA version being used.
- - Check using MIRA 3.4 (later versions have a different API)
-v0.0.6 - Tell MIRA to use /tmp for temporary files
- - Tell MIRA to ignore long read names (otherwise it aborts)
-
-
-Developers
-==========
-
-This script and related tools are being developed on the following hg branch:
-http://bitbucket.org/peterjc/galaxy-central/src/tools
-
-For making the "Galaxy Tool Shed" http://community.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder:
-
-tar -czf mira_wrapper.tar.gz tools/sr_assembly/mira.*
-
-Check this worked:
-
-$ tar -tzf mira_wrapper.tar.gz
-tools/sr_assembly/mira.py
-tools/sr_assembly/mira.txt
-tools/sr_assembly/mira.xml
-
-
-Licence (MIT/BSD style)
-=======================
-
-Permission to use, copy, modify, and distribute this software and its
-documentation with or without modifications and for any purpose and
-without fee is hereby granted, provided that any copyright notices
-appear in all copies and that both those copyright notices and this
-permission notice appear in supporting documentation, and that the
-names of the contributors or copyright holders not be used in
-advertising or publicity pertaining to distribution of the software
-without specific prior permission.
-
-THE CONTRIBUTORS AND COPYRIGHT HOLDERS OF THIS SOFTWARE DISCLAIM ALL
-WARRANTIES WITH REGARD TO THIS SOFTWARE, INCLUDING ALL IMPLIED
-WARRANTIES OF MERCHANTABILITY AND FITNESS, IN NO EVENT SHALL THE
-CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY SPECIAL, INDIRECT
-OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE
-OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE
-OR PERFORMANCE OF THIS SOFTWARE.
diff -r 4d3f94dfb857 -r 4266cccbb45a tools/sr_assembly/mira.xml
--- a/tools/sr_assembly/mira.xml Thu Feb 14 06:26:32 2013 -0500
+++ /dev/null Thu Jan 01 00:00:00 1970 +0000
@@ -1,156 +0,0 @@
-
- Takes Sanger, Roche, Illumina, and Ion Torrent data
- mira.py -v
- mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log
-##Give the wrapper script list of output filenames, then the mira command...
-mira --job=$job_method,$job_type,$job_quality
-
-##Input files
-#if $condBackbone.use == "true":
- ## Can this be linked to job_method as well? If mapping we need the backbone...
- -SB:lb=1:bft=fasta -FN:bbin=${condBackbone.filename}
-#end if
-#if $condSanger.use == "true":
- SANGER_SETTINGS
- ## Not easy in Galaxy to add sanger to --job, so use load_sequence_data(lsd) instead
- ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
- -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condSanger.filename}
-#end if
-#if $condRoche.use == "true":
- 454_SETTINGS
- ## Not easy in Galaxy to add 454 to --job, so use load_sequence_data(lsd) instead
- ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
- -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condRoche.filename}
-#end if
-#if $condIllumina.use == "true":
- SOLEXA_SETTINGS
- ## Not easy in Galaxy to add solexa to --job, so use load_sequence_data(lsd) instead
- -LR:lsd=1:ft=fastq -FN:fqi=${condIllumina.filename}
- ##TODO - Look at -LR FASTQ qual offset (fqqo)
-#end if
-#if $condIonTorrent.use == "true":
- IONTOR_SETTINGS
- ## Not easy in Galaxy to add iontor to --job, so use load_sequence_data(lsd) instead
- ## I expect hard trimmed FASTQ files with no NCBI traceinfo XML file
- -LR:lsd=1:mxti=0:ft=fastq -FN:fqi=${condIonTorrent.filename}
-#end if
-
-##Output files
-COMMON_SETTINGS
-
-##ignore warnings about long read names
--MI:somrnl=0
-
-##Explicitly request the FASTA (+QUAL), CAF, ACE, WIG output
-##Explicitly disable formats we won't use like MAF (reduce IO)
--OUT:orf=1:orc=1:ora=1:orw=1:orm=0:org=0:ors=0
-
-##remove_rollover_tmps, remove_tmp_directory
--OUT:rrot=1:rtd=1
-
-##put mira temp directory on local storage
--DI:trt=/tmp
-
-
-
-
-
-
-
-
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- Bio
- mira
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-**What it does**
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-Runs MIRA v3, collects the output, and throws away all the temporary files.
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-**Citation**
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-This tool uses MIRA. If you use this tool in scientific work leading to a
-publication, please cite:
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-Chevreux et al. (1999) Genome Sequence Assembly Using Trace Signals and Additional Sequence Information Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB) 99, pp. 45-56.
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