Mercurial > repos > dawe > srf2fastq
comparison srf2fastq/README @ 0:d901c9f41a6a default tip
Migrated tool version 1.0.1 from old tool shed archive to new tool shed repository
author | dawe |
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date | Tue, 07 Jun 2011 17:48:05 -0400 |
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-1:000000000000 | 0:d901c9f41a6a |
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1 This tool comes with io_lib (from Staden package) version 1.12.2 | |
2 io_lib is necessary as you will need srf2fastq executable; if you alread have the binary, skip the io_lib installation. | |
3 You may find a more recent version here http://sourceforge.net/projects/staden/files/ | |
4 | |
5 1- Install io_lib | |
6 cd io_lib-1.12.2 | |
7 ./configure --prefix=PREFIX | |
8 make | |
9 make install #assuming you have already superuser permissions granted | |
10 | |
11 2- Edit srf2fastq.sh | |
12 You will need to change the path of srf2fastq executable if | |
13 PREFIX has been defined different from /usr/local:wq | |
14 | |
15 3- Add support for SRF files in galaxy (if galaxy team hasn't added yet) | |
16 Here comes a series of diffs you may want to integrate. lib/galaxy/datatypes/binary.py and lib/galaxy/datatypes/registry.py | |
17 are part of galaxy distribution so a hg diff output is given. datatype_conf.xml is not in | |
18 galaxy repository (the sample is), so a unified diff is given (well, it's the same...) | |
19 | |
20 diff -r 60448575467f lib/galaxy/datatypes/binary.py | |
21 --- a/lib/galaxy/datatypes/binary.py Mon Aug 23 10:15:17 2010 -0400 | |
22 +++ b/lib/galaxy/datatypes/binary.py Wed Aug 25 10:26:38 2010 +0200 | |
23 @@ -222,3 +222,31 @@ | |
24 Binary.__init__( self, **kwd ) | |
25 self._magic = 0x8789F2EB | |
26 self._name = "BigBed" | |
27 + | |
28 +class Srf( Binary ): | |
29 + """ Illumina Sequence Archive (SRF) """ | |
30 + file_ext = "srf" | |
31 + | |
32 + def __init__( self, **kwd ): | |
33 + Binary.__init__( self, **kwd ) | |
34 + def sniff( self, filename ): | |
35 + try: | |
36 + header = open( filename ).read(4) | |
37 + if binascii.b2a_hex( header ) == binascii.hexlify( 'SSRF' ): | |
38 + return True | |
39 + return False | |
40 + except: | |
41 + return False | |
42 + def set_peek( self, dataset, is_multi_byte=False ): | |
43 + if not dataset.dataset.purged: | |
44 + dataset.peek = "Binary srf file" | |
45 + dataset.blurb = data.nice_size( dataset.get_size() ) | |
46 + else: | |
47 + dataset.peek = 'file does not exist' | |
48 + dataset.blurb = 'file purged from disk' | |
49 + def display_peek( self, dataset ): | |
50 + try: | |
51 + return dataset.peek | |
52 + except: | |
53 + return "Binary srf file (%s)" % ( data.nice_size( dataset.get_size() ) ) | |
54 + | |
55 | |
56 diff -r 60448575467f lib/galaxy/datatypes/registry.py | |
57 --- a/lib/galaxy/datatypes/registry.py Mon Aug 23 10:15:17 2010 -0400 | |
58 +++ b/lib/galaxy/datatypes/registry.py Wed Aug 25 10:28:01 2010 +0200 | |
59 @@ -173,6 +173,7 @@ | |
60 'sam' : tabular.Sam(), | |
61 'scf' : binary.Scf(), | |
62 'sff' : binary.Sff(), | |
63 + 'srf' : binary.Srf(), | |
64 'tabular' : tabular.Tabular(), | |
65 'taxonomy' : tabular.Taxonomy(), | |
66 'txt' : data.Text(), | |
67 @@ -213,6 +214,7 @@ | |
68 if len(self.sniff_order) < 1: | |
69 self.sniff_order = [ | |
70 binary.Bam(), | |
71 + binary.Srf(), | |
72 binary.Sff(), | |
73 xml.BlastXml(), | |
74 sequence.Maf(), | |
75 | |
76 diff -u datatypes_conf.xml datatypes_conf.xml.sample | |
77 --- datatypes_conf.xml 2010-08-25 10:32:46.778959931 +0200 | |
78 +++ datatypes_conf.xml.sample 2010-08-25 07:20:34.190956591 +0200 | |
79 @@ -105,7 +105,6 @@ | |
80 <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true"/> | |
81 <datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/> | |
82 <datatype extension="sff" type="galaxy.datatypes.binary:Sff" mimetype="application/octet-stream" display_in_upload="true"/> | |
83 - <datatype extension="srf" type="galaxy.datatypes.binary:Srf" mimetype="application/octet-stream" display_in_upload="true"/> | |
84 <datatype extension="taxonomy" type="galaxy.datatypes.tabular:Taxonomy" display_in_upload="true"/> | |
85 <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/> | |
86 <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/> | |
87 @@ -264,7 +263,6 @@ | |
88 and so on. | |
89 --> | |
90 <sniffer type="galaxy.datatypes.binary:Bam"/> | |
91 - <sniffer type="galaxy.datatypes.binary:Srf"/> | |
92 <sniffer type="galaxy.datatypes.binary:Sff"/> | |
93 <sniffer type="galaxy.datatypes.xml:BlastXml"/> | |
94 <sniffer type="galaxy.datatypes.sequence:Maf"/> |