| Previous changeset 8:4266cccbb45a (2013-04-24) Next changeset 10:a2fb1e67bd11 (2014-01-30) |
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Commit message:
Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub. |
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modified:
tools/mira_3_4/mira.xml |
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added:
test-data/tvc_contigs.fasta test-data/tvc_mini.fastq tools/mira_3_4/README.rst tools/mira_3_4/tool_dependencies.xml |
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removed:
tools/mira_3_4/mira.txt |
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| diff -r 4266cccbb45a -r 5573d802e431 test-data/tvc_contigs.fasta --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tvc_contigs.fasta Wed Sep 18 06:22:19 2013 -0400 |
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| @@ -0,0 +1,20 @@ +>mira_c1 +ttagcgtggtcgcggccgaggtaccctctaccatgaaaccaggcttgggtccctctggct +gtctcttggtgctgataatcttaccttgtgccttggcctcagccttcaacttatcgttct +tcttgatcctctccatgatctcctcatggcaccttgatggctggacatgttccacacgaa +catgaatcctcttccttatgattctgtttccaacctgcttgttgacctcaacaccaacag +cacgcttggtgacgttccatacccgacccgtgcggccatgatagaacttgtggggcatac +ctttgtggatcgacccgttaaccttgacatcaacatagtcgccgactttgaagatacgaa +ggtaagttgtgagatgggtaggacccttcttcctgaatgcccgagcaaatagatctctgg +tgcgcgaccccaaaccgtgacccgccggcattttgcggtgtttttcagacctgcccgggc +ggccgctcgaaa +>mira_c2 +tttcgagcggycgcccggscgaggtaccctscaccatgaaaccaggcttgggtccctcwg +gctgyctcttggtgctgataatcttwccytgtgccttkgcctcagccttcaacttatcrt +tcttcttgatcctctccattatctcctcatggcamckagatggctggacatgttccacac +gaacatgaatcctcttccttatgattctgtttccaacctgyttgttgacctcaacaccaa +cagcgcgcttggtgacgttccatacccgacccgtgcggccatggtagaacttgtggggca +tacctttgtggatcgacccgttaaccttgacatcaacatagtcgccgactttgaagatac +gaaggtaagttgtgagatgggtaggacccttcttcctgaatgcccgagcaaatagatccc +tggtgcgtgacctcaaaccgtgacccgccggcattttgaggtgtttttcagacctgcccg +ggcggccgctcgaaa |
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| diff -r 4266cccbb45a -r 5573d802e431 test-data/tvc_mini.fastq --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tvc_mini.fastq Wed Sep 18 06:22:19 2013 -0400 |
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| b"@@ -0,0 +1,24 @@\n+@gnlti136477918\n+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTACCCTCCACCATGAAACCAGGCTTGGGTCCCTCAGGCTGCCTCTTGGTGCTGATAATCTTTCCCTGTGCCTTTGCCTCAGCCTTCAACTTATCATTCTTCTTGATCCTCTCCATTATCTCCTCATGGCAACGAGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATCCTGTTACCAACCTGTTTGTTGACCTCAACACCAACAGCGCGCTTGGTAACATTCCAGACCCGACCCGTGCGCCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGAACTCAAACCGTGACCCGCCGGCATTTTGAGGTGTTTTTCAGCTGCCTTGTTCACXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n++\n+38<>><><<96-++42:AABBCCCCCCCCDFFFIYYIIIIIINTTTTNNNNNNTTTTTTNNIIIIHHHHHHYIFFFIDIINIITTTOQDDDHHHNTYTFFFIIINNIITDDDDDDFLLTTTLLLYYYYYYFFIIIILKOOYYYNNNNNNOOKKKKILLLFFIOOTTNLLLLLNYYYYKYFDDDLLLNNNTTNNLMKKSYNNJIIGGGGLLIILOOYYYYYYYYYTNNNNNTYYYYYYYTOLLLLLLNTTYYTTTLLTYYKKKONNNNLLLLGGINIIIIIINNNNNNNNIHHHHHHHHHHINIITTTTNNNNNTYTNNNNIIIFFDHHHFFINNNNIHHHDDEIDDDNNDDKQQQQMMMQQYYNNIDCBBBBAHIGGGKYYYOOD?<AACCCCCHCCC@>>>>HBBAAAA>@999AOOOYIIICC<<,,,99HHHFKK??C>>B>>H?6/+))42856301:7<>HHEI4/))-10449--0..((*4))*35A<9+++44>BB754---@<;42*))45:7024.(')))')++049>>41-'(,'(.2393222/3171((((-.4011/0+).)''),..4133><B=451119411+))<44:686:/066888888=::884))*'''**,''*-.''*,/2(*144+')64>;1/,'')''1*30+0..****(*0-.4-)*),'(''+,-((*+))**+,''''''***''***-*)121,''''(+*,,+-((****.0..,0*))*(),))''))*+,*)()))''''+'')'')**)()'','')'(**((*((*(((*441.-*****())+*''')-++*****-*((((**))))))*)))++***)(**11.()****0*-,((*--.***,((,,,**'')'''')'-((--,''**441***)+'(''*,*(\n+@gnlti136478624\n+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAGCGTGGTCGCGGCCGAGGTACCCTCTACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCACGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGATAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGGCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGGCCGAGCAAATAGATCTCTGGGTGCGGGAACTCAAACCGGGAACCGGCGGCATTTTGCGGTGTTTTTAGACCCTGCCGGGGGGGCGGTCGAAAGGCCGATTCTTGAGATTTTCCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGGGGGTAGGAGGTTGTAATTGGAAAAACCTGGGGTAGCAAGTTAATGGCTTGAGCAATTCCGTTCGGCGGGTGGGTATAGAGAAGGGGCGGGCGATCGGGATCCGAAGATGGGGAGCGGATGGGGAGGAGAGGCAGGTGGGGATATAGGGGGGGGGTGGGGTAGGGGAGGGGCGGTGCTGTAGGGGGAGGGGCGGCGTTGGTTTTCTGTGTTACGAGTTGGGTGACCCGAAGTAATTGGGG\n++\n++1449>>>;=::AADDCCCCFIICCBB>???BBDDDDYYHBCCBBFF@@777BBG@>7584;;@DHDDDDDDMNIIIIIYYYTOYKKKMIDDDDDHOKKKQSTTTNNIIYYFFFFFIDDDDDIYOOIIDAA>DADDFDLLDDDIKKKKOKKKKKKYYYOOJJJOYYYYTOOKKPMMMMMSSSSMMMSSYYYYLJIIIID=====FKKKKKKYYYOOKKIIIIISSFFDIHIIKSSTOOKKKLYYSSKMIIIOOIIIDDDDHDDDIOOIIFFFIIIIKKKMIIIIIIMKKKKIIIFDDDDADDIDDDDDDDHDDDDFFF99///<<HFFFFFFFFGOOYTDDDHHH99,,,95>>>>47//-</3-822.446777BBBFFIOC>6.++-53:?:>7744213...772007:9:-++33>>DH>>??933;;FQ<93/+10++/.//-10234:1//223;:/,,***++'')'+,/)))-.2.++((.0***,))*,0(())''))))+'')***''))***))),669+,*****..''')*,**,*))))*'',)))'(++,++((*+*)*.*))''')***''.*))'')''''''***+)))++**(''''')****)''')'(***''**+/.)))*)')((''***(('')'')-))''''.'')))**'+''''**))''))***+((***)%(((***(((((,.,,(((((*(((+.(()'''')*(())(***((**-+,,)')''*/,''''**'''))((''*+((''''))*))'')'')),.)())'''''('*)**+***-*(')''))((+++0***(('')'')**()++*+**(')).5+*'''')*,---'''')'''\n+@gnlti136478626\n+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCTCAAAATGCCGGCGGGTCACGGTTTGAGGTCACGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGCGCTGTT"..b"TGGGTGTGGGGGTGGGTTTTGTTAGGCGAGGTGGTTTTTTTTTCTTTTTTTTTTTAGTGGAGGTGT\n++\n+04--46:<<B<<>@>HHEB<822<<IEHIHCCCCCCIIIITTIIIIIINNTTTTTYTIHHHHHHNNNIIDDDDFFNTKM>>?OQFFFMKOOTFDDDDHHIIIIOHFFFFFINTDDAAAADHHDDDOYNNHHFFDDDDDDFDC=AA=DIIIIFFNHHFFFFNNNNNNNNNNDD448DNTOOKKKOBB?DFGGGNOTOO555>>A>>>AAF:::>>@DB=====5AACOIIBCCBB<5005<41''+18EAAAHHHB>96-+,+14:AAIB??>>CD>>;87>5:30-14477<>@CDDD>>?==MQYI>H---88:77:<B>>=33000008<9::>BBBFHHCCC>IFDDDOOOQIQQII:2((+6<552228>DDDEH>>33399>31)''-.FFIMIIIO>>333;@II>71:37<AAEIAA778<B69,,,01BBIKFF>>>944,,,6:6/(((*44<<43,,,66AEH98,,,6/+**--..((*,1><::65/0*'))'(,-,)++*31+((*((**.,+*'')'()'''*++))''('*+26410''''+)(())''))*'(***++*))*((****(''''')++**)+'')*))*.-***))*)*-/****,-30.)''''''''***''''')-.*))'')''**++*))/,,((,+-***+)'''''')+'''.*)')'(0-+((+++)))'''(*+'''')'(**,***''''))*))'')))),''))''))*((***))/()(*''''++**((((((****(')))))*))'),))'')''.)))))))'')+,++')-))'(+))***))''))****++))))+1-**))**'(140''))**))'')+**(\n+@gnlti136479357\n+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTGTGGTCGCGGCCGAGGTACCCTGCACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCGCGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGGACTCCAAACGTGAACTTGCCGGGCGGGGGGGAGAGGGGGAGCGGGGGGGGGGGAGAATAAGGGGGGAGGGGAGGGGGAGAGAAAAGGGAGGAGGGGGGGGGTAGGGAGGGAGAGGGAGGGGGGAGGGGGGGGGAGGGGGGGGGGGGAGGGAAGGGGGGGGAGGGGGGGAGGGGGAGGGGAGAGGGGGAGGGGAGGGGGGGGGGAGGGGAGGGGAAGAGGGGGGGGGGGGGGGGGGGAGGGGGGGAGGGGGGGGGGGAGGGGGGGGGGGGGGAGGGAGAAGGAGAAA\n++\n+.4<BB;>>>>>>>>FDCCCCCCIINIIIDCCCCCCDDDDYQKKFNNNCAAAAAINNIIINTIIHHDDDDDDDDDDDKITTTTLYYYYYLFFIIIILOKKKIIIIKKOKYFDDDDDFIIIIIKKKLLLLTIDDDDDFFDDDDDNNIIIIIKKDDDDHHJOYYSSMMFFADDDDLYSSB>666>BDDDDKOOKJJOOJJED==99AOIJJOOYYYLJJJLLTTTTLYYYYYYYYYYLLIIBBADDNOIIIIIINDAADDDDKOOIIIIIFDDA>7==@@DII??887BBOOFDDDDDIYYNNNHDDKOO?BBHHINODDAF>A>AADFFIIOGFFFFIITOOIDDDDDDDDDDDHHD89,,,<>FFFDD>99<<<B<845;<BAAA;>99=EBIIIIIOOD@@><>AB<8::AA:>AABHIHHHCCC99--+46CCCIIIIAA551-4440++)))4499+))019<>>>1/()0/-('''129.,//+((**+++8@@,*)11))*+***+++))%(,.*)))..,.2+**+8..)))),*))'')))''.''+)*++)+)))''))'(++++*))'''''))****))''))/.03:=741.''**),''''**))))))4**)')'').11.('*))'%)*-.2))*.0('''))(')''))****))('+'')''))****,((((**))1..''))***)1-1-.''),,''))%(.**)(')))*)-().-.***))1)''+''))****))''\n+@gnlti136479522\n+XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCGCAAAATGCCGGCGGGTCACGGTTTGGGGTCGCGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTATCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGTGCTGTTGGGTGTNGAGGTCAAAAGCAAGTTGGAAACAGAATCATAAGGAAGAGGATTCATGTCCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGGAGAGGATCAAGAAGAACGATTAAGTGAAGGCTGAGGGCAAGGCACAAGGTATGATTATCAGGACCAAGAGACAGGCAGAGGGGACCAAGGCCTGGTTTCATGGGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX\n++\n+(/..2>>H@CACCHICCCCCCIIYTTTFA>>>ADIIIIOTNNNNNIKINIIHDDDIIIHOMMFNNHDDDDDFINIIKOKKKFFIIIITYTLYIIIIIINTTTIFFFFFKLLYYYYYNNNNHHDDDGGNYYYYYYFDGDDDTHIIIIIIIKFFFIIITYINIIIITTTTYYYYTTNNNNNNNIIIIIIIIIFFIOOOOOIFFFFIIINOFKKNND84**+::FFFDHDDDDDIDD>44***49IIIFCIA?94233AIIIMQOOBFF:4-***66CCCCD>>444>?B44*((***45C>@BHIAAAA94%!%44=1-''''))''+(+/,((*245411.40)((+4::79..***-+/.()14BEEIIBCFIIHD88,,,NBID>>A>BB?AAAA>H:::;::4-+,,4/;46,**4841))/1.''*)))+444+++520'')11)(*.+,0**0((*159501224594406652//-/-2,/*1*')+.()./1.01::>>>>5511.4***1:5*((,-/-((******+*-'')((/20-)-,-*++.1/.(())''),351''))'(..280.'')+()**,398..''))**((+1.(())''))**-.--,,**''*)((-)***(()),1,/.1,))))+,+*+*++,-,'''')**((+*++,))))''))**1.,,***+****,+**+++4***.*))'')'')))''))*.5811.--+,+*+*))+,,-..+\n" |
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| diff -r 4266cccbb45a -r 5573d802e431 tools/mira_3_4/README.rst --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira_3_4/README.rst Wed Sep 18 06:22:19 2013 -0400 |
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| @@ -0,0 +1,123 @@ +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 (MIT licence). + +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). + +It is available from the Galaxy Tool Shed at: +http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler + + +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:: + + <tool file="mira_3_4/mira.xml" /> + +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 +======= + +======= ====================================================================== +Version Changes +------- ---------------------------------------------------------------------- +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 <version_command> 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. +v0.0.8 - Basic unit test added (but commented out due to Galaxy issue). + - Link to Tool Shed added to help text and this documentation. + - Use reStructuredText for this README file. + - Adopted standard MIT licence. + - Updated citation information (Cock et al. 2013). + - Development moved to GitHub, https://github.com/peterjc/pico_galaxy +======= ====================================================================== + + +Developers +========== + +This script and related tools were initially developed on the following hg branch: +http://bitbucket.org/peterjc/galaxy-central/src/tools + +Development has now moved to a dedicated GitHub repository: +https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4 + +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/README.rst tools/mira_3_4/mira.xml tools/mira_3_4/mira.py tools/mira_3_4/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta + +Check this worked:: + + $ tar -tzf mira_wrapper.tar.gz + tools/mira_3_4/README.rst + tools/mira_3_4/mira.xml + tools/mira_3_4/mira.py + tools/mira_3_4/tool_dependencies.xml + test-data/tvc_mini.fastq + test-data/tvc_contigs.fasta + + +Licence (MIT) +============= + +Permission is hereby granted, free of charge, to any person obtaining a copy +of this software and associated documentation files (the "Software"), to deal +in the Software without restriction, including without limitation the rights +to use, copy, modify, merge, publish, distribute, sublicense, and/or sell +copies of the Software, and to permit persons to whom the Software is +furnished to do so, subject to the following conditions: + +The above copyright notice and this permission notice shall be included in +all copies or substantial portions of the Software. + +THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR +IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, +FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE +AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER +LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, +OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN +THE SOFTWARE. |
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| diff -r 4266cccbb45a -r 5573d802e431 tools/mira_3_4/mira.txt --- a/tools/mira_3_4/mira.txt Wed Apr 24 12:43:17 2013 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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| @@ -1,104 +0,0 @@ -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: - -<tool file="mira_3_4/mira.xml" /> - -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 <version_command> 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. |
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| diff -r 4266cccbb45a -r 5573d802e431 tools/mira_3_4/mira.xml --- a/tools/mira_3_4/mira.xml Wed Apr 24 12:43:17 2013 -0400 +++ b/tools/mira_3_4/mira.xml Wed Sep 18 06:22:19 2013 -0400 |
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| @@ -1,7 +1,12 @@ -<tool id="mira_assembler" name="Assemble with MIRA" version="0.0.6"> +<tool id="mira_assembler" name="Assemble with MIRA v3.4" version="0.0.8"> <description>Takes Sanger, Roche, Illumina, and Ion Torrent data</description> - <version_command interpreter="python">mira.py -v</version_command> - <command interpreter="python">mira.py mira $out_fasta $out_qual $out_ace $out_caf $out_wig $out_log + <requirements> + <requirement type="python-module">Bio</requirement> + <requirement type="binary">mira</requirement> + <requirement type="package" version="3.4.1.1">MIRA</requirement> + </requirements> + <version_command interpreter="python">mira.py -v</version_command> + <command interpreter="python">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 @@ -52,7 +57,7 @@ -DI:trt=/tmp </command> - <inputs> + <inputs> <param name="job_method" type="select" label="Assembly method" help="Mapping mode requires backbone/reference sequence(s)"> <option value="denovo">De novo</option> <option value="mapping">Mapping</option> @@ -124,32 +129,63 @@ <param name="filename" type="data" format="fastq" label="Ion Torrent reads file" help="FASTQ format" /> </when> </conditional> - </inputs> - <outputs> - <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> - <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> - <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> - <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> - <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> - <data name="out_log" format="txt" label="MIRA log" /> - </outputs> - <tests> - </tests> - <requirements> - <requirement type="python-module">Bio</requirement> - <requirement type="binary">mira</requirement> - </requirements> - <help> + </inputs> + <outputs> + <data name="out_fasta" format="fasta" label="MIRA contigs (FASTA)" /> + <data name="out_qual" format="qual454" label="MIRA contigs (QUAL)" /> + <data name="out_caf" format="txt" label="MIRA contigs (CAF)" /> + <data name="out_ace" format="txt" label="MIRA contigs (ACE)" /> + <data name="out_wig" format="wig" label="MIRA coverage (Wiggle)" /> + <data name="out_log" format="txt" label="MIRA log" /> + </outputs> + <tests> + <!-- Based on the MIRA v3.4.1.1 bundled minidemo/estdemo2 which uses + strain data and miraSearchESTSNPs. Here we just assemble it. --> +<!-- +Commenting out test until Galaxy framework is fixed, +https://trello.com/c/zSTrfDOB/820-disambiguated-conditional-parameters-not-supported-in-unit-tests + <test> + <param name="job_method" value="denovo" /> + <param name="job_type" value="est" /> + <param name="job_qual" value="accurate" /> + <param name="condBackbone.use" value="false" /> + <param name="condSanger.use" value="true" /> + <param name="condSanger.filename" value="tvc_mini.fastq" ftype="fastq" /> + <param name="condRoche.use" value="false" /> + <param name="condIllumina.use" value="false" /> + <param name="condIonTorrent.use" value="false" /> + <output name="out_fasta" file="tvc_contigs.fasta" ftype="fasta" /> + </test> +--> + </tests> + <help> **What it does** Runs MIRA v3.4, collects the output, and throws away all the temporary files. +MIRA is an open source assembly tool capable of handling sequence data from +a range of platforms (Sanger capillary, Solexa/Illumina, Roche 454 and also +Ion Torrent). + +It is particularly suited to small genomes such as bacteria. + **Citation** -If you use this tool in scientific work leading to a publication, please cite: +If you use this Galaxy tool in work leading to a scientific publication please +cite the following papers: + +Peter J.A. Cock, Björn A. Grüning, Konrad Paszkiewicz and Leighton Pritchard (2013). +Galaxy tools and workflows for sequence analysis with applications +in molecular plant pathology. PeerJ 1:e167 +http://dx.doi.org/10.7717/peerj.167 -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. +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. - </help> +This wrapper is available to install into other Galaxy Instances via the Galaxy +Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler + + </help> </tool> |
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| diff -r 4266cccbb45a -r 5573d802e431 tools/mira_3_4/tool_dependencies.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/mira_3_4/tool_dependencies.xml Wed Sep 18 06:22:19 2013 -0400 |
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| @@ -0,0 +1,25 @@ +<?xml version="1.0"?> +<tool_dependency> + <package name="MIRA" version="3.4.1.1"> + <install version="1.0"> + <actions> + <!-- Sourceforge doesn't offer nice clean download URLs which is a shame --> + <action type="download_by_url">http://downloads.sourceforge.net/project/mira-assembler/MIRA/stable/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fmira-assembler%2Ffiles%2FMIRA%2Fstable%2F&ts=1366819213&use_mirror=kent</action> + <!-- Currently we only need the main binary itself, mira --> + <action type="move_file"><source>mira_3.4.1.1_prod_linux-gnu_x86_64_static/bin/mira</source><destination>$INSTALL_DIR/</destination></action> + <action type="set_environment"> + <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable> + </action> + </actions> + </install> + <readme> +Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries +for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could +use if/when the Galaxy installation framework allow that kind of flexibility. + +http://chevreux.org/projects_mira.html +http://sourceforge.net/projects/mira-assembler/ + </readme> + </package> +</tool_dependency> + |