# HG changeset patch # User peterjc # Date 1379499739 14400 # Node ID 5573d802e43193f36b9f2db55a70d82f80829139 # Parent 4266cccbb45aa3360b83c159ac111f3286f0d5e3 Uploaded v0.0.8, MIT licence, RST for README, citation information, development moved to GitHub. 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 @@ -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 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 @@ -0,0 +1,24 @@ +@gnlti136477918 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTACCCTCCACCATGAAACCAGGCTTGGGTCCCTCAGGCTGCCTCTTGGTGCTGATAATCTTTCCCTGTGCCTTTGCCTCAGCCTTCAACTTATCATTCTTCTTGATCCTCTCCATTATCTCCTCATGGCAACGAGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATCCTGTTACCAACCTGTTTGTTGACCTCAACACCAACAGCGCGCTTGGTAACATTCCAGACCCGACCCGTGCGCCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGAACTCAAACCGTGACCCGCCGGCATTTTGAGGTGTTTTTCAGCTGCCTTGTTCACXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ++ +38<>><><<96-++42:AABBCCCCCCCCDFFFIYYIIIIIINTTTTNNNNNNTTTTTTNNIIIIHHHHHHYIFFFIDIINIITTTOQDDDHHHNTYTFFFIIINNIITDDDDDDFLLTTTLLLYYYYYYFFIIIILKOOYYYNNNNNNOOKKKKILLLFFIOOTTNLLLLLNYYYYKYFDDDLLLNNNTTNNLMKKSYNNJIIGGGGLLIILOOYYYYYYYYYTNNNNNTYYYYYYYTOLLLLLLNTTYYTTTLLTYYKKKONNNNLLLLGGINIIIIIINNNNNNNNIHHHHHHHHHHINIITTTTNNNNNTYTNNNNIIIFFDHHHFFINNNNIHHHDDEIDDDNNDDKQQQQMMMQQYYNNIDCBBBBAHIGGGKYYYOOD?>>>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>;1/,'')''1*30+0..****(*0-.4-)*),'(''+,-((*+))**+,''''''***''***-*)121,''''(+*,,+-((****.0..,0*))*(),))''))*+,*)()))''''+'')'')**)()'','')'(**((*((*(((*441.-*****())+*''')-++*****-*((((**))))))*)))++***)(**11.()****0*-,((*--.***,((,,,**'')'''')'-((--,''**441***)+'(''*,*( +@gnlti136478624 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAGCGTGGTCGCGGCCGAGGTACCCTCTACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCACGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGATAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGGCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGGCCGAGCAAATAGATCTCTGGGTGCGGGAACTCAAACCGGGAACCGGCGGCATTTTGCGGTGTTTTTAGACCCTGCCGGGGGGGCGGTCGAAAGGCCGATTCTTGAGATTTTCCXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXGGGGGTAGGAGGTTGTAATTGGAAAAACCTGGGGTAGCAAGTTAATGGCTTGAGCAATTCCGTTCGGCGGGTGGGTATAGAGAAGGGGCGGGCGATCGGGATCCGAAGATGGGGAGCGGATGGGGAGGAGAGGCAGGTGGGGATATAGGGGGGGGGTGGGGTAGGGGAGGGGCGGTGCTGTAGGGGGAGGGGCGGCGTTGGTTTTCTGTGTTACGAGTTGGGTGACCCGAAGTAATTGGGG ++ ++1449>>>;=::AADDCCCCFIICCBB>???BBDDDDYYHBCCBBFF@@777BBG@>7584;;@DHDDDDDDMNIIIIIYYYTOYKKKMIDDDDDHOKKKQSTTTNNIIYYFFFFFIDDDDDIYOOIIDAA>DADDFDLLDDDIKKKKOKKKKKKYYYOOJJJOYYYYTOOKKPMMMMMSSSSMMMSSYYYYLJIIIID=====FKKKKKKYYYOOKKIIIIISSFFDIHIIKSSTOOKKKLYYSSKMIIIOOIIIDDDDHDDDIOOIIFFFIIIIKKKMIIIIIIMKKKKIIIFDDDDADDIDDDDDDDHDDDDFFF99///<>>>47//-6.++-53:?:>7744213...772007:9:-++33>>DH>>??933;;FQ<93/+10++/.//-10234:1//223;:/,,***++'')'+,/)))-.2.++((.0***,))*,0(())''))))+'')***''))***))),669+,*****..''')*,**,*))))*'',)))'(++,++((*+*)*.*))''')***''.*))'')''''''***+)))++**(''''')****)''')'(***''**+/.)))*)')((''***(('')'')-))''''.'')))**'+''''**))''))***+((***)%(((***(((((,.,,(((((*(((+.(()'''')*(())(***((**-+,,)')''*/,''''**'''))((''*+((''''))*))'')'')),.)())'''''('*)**+***-*(')''))((+++0***(('')'')**()++*+**(')).5+*'''')*,---'''')''' +@gnlti136478626 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCTCAAAATGCCGGCGGGTCACGGTTTGAGGTCACGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTACCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGCGCTGTTGGTGTTGAGGTCAAGCATGAGGTGGGAAACAGAATCATAAGGAAAAGGATTCATGTGCGTGTGGAAGATGGTCAGGGATCGAGGTGCCATGAGGAGATCATGGTGAGGATCGAGAAGAACGATTAAGGGGAAGGCTGAGGGCGAGGGACAAGGTAAGATTATCAGCGACAAGAGACAAGCGGAGGGAGCCACGGCTGGGTGTGTGGTAGAGGGTGCCTCGGGCCGGGGCAAGGCTAAGCCGAATGCTGGGGATATTCATTAGACTGGGGGGCGGTCGAGGGTGGGTCGTAATGGGCCATTTGCGCGTATGGTGGGGTTGTTTGACATTGCGCTGGCCTCGGTTTACAGGGTTGTGATTGGAAAGCCGTGCGGTTGCCAACGTTAGTGTTTGGGAGACGTTCGCGTTCGGGGGCTGGGGTATTAAGGGGGGTCTGGGGTAAGGGCGTGCGAGGATGGTGGAGGGGTTTGGGGTTGGGCGTCTGTTTCGGGGTTTGTGGCGGGGGGTTGGTGGTTGCGTGACGGTGGGGGGGTTGGGCAGGCTATGGCGGGGCGTGGTGTTGGTCTGGTTGTGAGGATGTGAGTGTGCGTTGTTGTGTATTGGGACAGGT ++ +))..28:>C>CDDDDDDCCCCDDD>>A990028>HFFFIIFDDDDDHOTYYNGFAAAA;>??BQQIDDDIDIIIIGMMDDDDDDNIIIGGFFFFIMYKKIKKDD>D>>>C>D>><<<>::..'')46>IIIQIYYYMFDDAADKKKKYYYYYYNNDDDDIIGGKK777MMFFFKDDFAADDDDFKKKKFFFKIDDDDDDKIIIIEMFF=@@@B@BB??>O???OOTTTTLLKKK???DDDD>AAAA>B994B122:=B44/--447<155>>IIFFIKKKGGGGIIN944499C>>>>>>9D>D74-++.15;911**+/-''))****-,''))1.2-.*****-<>71+**()+19:46.--+-*1611+*((****'''''(-/411-1***.((+***('**-8211,-**'''')+,,4,))''))))'')),,(')))).5++))'')).1-+,,.-+(''(++,,,('''))*''''))')+).''))*)-('')+)*((++.+++-*))('))''))+-0./,,))''))'')''*'')))''****.+*''*))'')'')'')))**+++))'''))'''*''*((****'''')'(,(''''''')*''))''))++*(((*((-))'')-)**()******042))***((*))''))*,-.((*)'')%%%)+++****((***-+*)''''))))''''))''''''')))),))***+('))))+.,)()+**''+.-)))(')''))'(***,(((,,***((((**++'')'(*))'''(**'''******((****//--))0+)''))*****))'')%%'')('*)))-(*01**))'(( +@gnlti136479063 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTAGCGTGGTCGCGGCCGAGGTACCCTCTACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCGCGCTTGGTGACGTTCCATACCCGACCCGTGCGCCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGGCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGGCCGAGCAAATAGATCCCTGGTGCGTGAGCTCAAAGCGTGGACCGGCGGCATTTTAGGGTGTTTTTCAGCTGGCTCGGTGGTTTGAATGTGACTTGGGCGGGGGGGGGGTCGAAAGGCGAATTTGGAGATTTTCATAAAATTGGGGCGGTTGAAGATTGATTTTAAGGGGCAATTTGGGCTATAGGGGTGGTTTTAAATTAATGGGGGTGGTTTAAAAGTGTGATGGGGAAACGTGGGTTACCAATTTATGGGTGTGTGGAGTTCCCTTTGTGAGGTGGTATAGGAAAGGGGGGGCGTGACCTGCCACGTGGGGGGGGAAGTGTATGGGGGCGGGTTGGGGGGTTGAGGGGGGTGTGGGTGTGGGGGTGGGTTTTGTTAGGCGAGGTGGTTTTTTTTTCTTTTTTTTTTTAGTGGAGGTGT ++ +04--46:<@>HHEB<822<>?OQFFFMKOOTFDDDDHHIIIIOHFFFFFINTDDAAAADHHDDDOYNNHHFFDDDDDDFDC=AA=DIIIIFFNHHFFFFNNNNNNNNNNDD448DNTOOKKKOBB?DFGGGNOTOO555>>A>>>AAF:::>>@DB=====5AACOIIBCCBB<5005<41''+18EAAAHHHB>96-+,+14:AAIB??>>CD>>;87>5:30-14477<>@CDDD>>?==MQYI>H---88:77:>=33000008<9::>BBBFHHCCC>IFDDDOOOQIQQII:2((+6<552228>DDDEH>>33399>31)''-.FFIMIIIO>>333;@II>71:37>>944,,,6:6/(((*44<<43,,,66AEH98,,,6/+**--..((*,1><::65/0*'))'(,-,)++*31+((*((**.,+*'')'()'''*++))''('*+26410''''+)(())''))*'(***++*))*((****(''''')++**)+'')*))*.-***))*)*-/****,-30.)''''''''***''''')-.*))'')''**++*))/,,((,+-***+)'''''')+'''.*)')'(0-+((+++)))'''(*+'''')'(**,***''''))*))'')))),''))''))*((***))/()(*''''++**((((((****(')))))*))'),))'')''.)))))))'')+,++')-))'(+))***))''))****++))))+1-**))**'(140''))**))'')+**( +@gnlti136479357 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTGTGGTCGCGGCCGAGGTACCCTGCACCATGAAACCAGGCTTGGGTCCCTCTGGCTGTCTCTTGGTGCTGATAATCTTACCTTGTGCCTTGGCCTCAGCCTTCAACTTATCGTTCTTCTTGATCCTCTCCATGATCTCCTCATGGCACCTTGATGGCTGGACATGTTCCACACGAACATGAATCCTCTTCCTTATGATTCTGTTTCCAACCTGCTTGTTGACCTCAACACCAACAGCGCGCTTGGTGACGTTCCATACCCGACCCGTGCGGCCATGGTAGAACTTGTGGGGCATACCTTTGTGGATCGACCCGTTAACCTTGACATCAACATAGTCGCCGACTTTGAAGATACGAAGGTAAGTTGTGAGATGGGTAGGACCCTTCTTCCTGAATGCCCGAGCAAATAGATCCCTGGTGCGTGGACTCCAAACGTGAACTTGCCGGGCGGGGGGGAGAGGGGGAGCGGGGGGGGGGGAGAATAAGGGGGGAGGGGAGGGGGAGAGAAAAGGGAGGAGGGGGGGGGTAGGGAGGGAGAGGGAGGGGGGAGGGGGGGGGAGGGGGGGGGGGGAGGGAAGGGGGGGGAGGGGGGGAGGGGGAGGGGAGAGGGGGAGGGGAGGGGGGGGGGAGGGGAGGGGAAGAGGGGGGGGGGGGGGGGGGGAGGGGGGGAGGGGGGGGGGGAGGGGGGGGGGGGGGAGGGAGAAGGAGAAA ++ +.4>>>>>>>FDCCCCCCIINIIIDCCCCCCDDDDYQKKFNNNCAAAAAINNIIINTIIHHDDDDDDDDDDDKITTTTLYYYYYLFFIIIILOKKKIIIIKKOKYFDDDDDFIIIIIKKKLLLLTIDDDDDFFDDDDDNNIIIIIKKDDDDHHJOYYSSMMFFADDDDLYSSB>666>BDDDDKOOKJJOOJJED==99AOIJJOOYYYLJJJLLTTTTLYYYYYYYYYYLLIIBBADDNOIIIIIINDAADDDDKOOIIIIIFDDA>7==@@DII??887BBOOFDDDDDIYYNNNHDDKOO?BBHHINODDAF>A>AADFFIIOGFFFFIITOOIDDDDDDDDDDDHHD89,,,<>FFFDD>99<<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)''+''))****))'' +@gnlti136479522 +XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTTCGAGCGGCCGCCCGGGCAGGTCTGAAAAACACCGCAAAATGCCGGCGGGTCACGGTTTGGGGTCGCGCACCAGAGATCTATTTGCTCGGGCATTCAGGAAGAAGGGTCCTACCCATCTCACAACTTACCTTCGTATCTTCAAAGTCGGCGACTATGTTGATGTCAAGGTTAACGGGTCGATCCACAAAGGTATGCCCCACAAGTTCTATCATGGCCGCACGGGTCGGGTATGGAACGTCACCAAGCGTGCTGTTGGGTGTNGAGGTCAAAAGCAAGTTGGAAACAGAATCATAAGGAAGAGGATTCATGTCCGTGTGGAACATGTCCAGCCATCAAGGTGCCATGAGGAGATCATGGAGAGGATCAAGAAGAACGATTAAGTGAAGGCTGAGGGCAAGGCACAAGGTATGATTATCAGGACCAAGAGACAGGCAGAGGGGACCAAGGCCTGGTTTCATGGGTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX ++ +(/..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.--+,+*+*))+,,-..+ 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 @@ -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:: + + + +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 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. 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 @@ -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: - - - -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 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 @@ -1,7 +1,12 @@ - + 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 + + Bio + mira + MIRA + + 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 @@ -52,7 +57,7 @@ -DI:trt=/tmp - + @@ -124,32 +129,63 @@ - - - - - - - - - - - - - Bio - mira - - + + + + + + + + + + + + + + **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. - +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 + + 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 @@ -0,0 +1,25 @@ + + + + + + + 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 + + mira_3.4.1.1_prod_linux-gnu_x86_64_static/bin/mira$INSTALL_DIR/ + + $INSTALL_DIR + + + + +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/ + + + +