1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
|
SeqAn for Debian
================
Quoting upstream namely Manuel Holtgrewe <manuel.holtgrewe@fu-berlin.de>
in a private mail to Andreas Tille <andreas@fam-tille.de> and
Filippo Rusconi <lopippo@debian.org> at Wed, 27 Nov 2013 09:38:30 +0100:
The SeqAn apps are a pretty diverse collection. Some are just simple
tools for Bioinformaticians, some are results from our research. The
tools should be useful for useful but from the research result, only
some are. I would suggest placing the following binaries in /usr/bin
since they are tools useful for and used by users/scientists:
alf
gustaf
insegt
masai_indexer
masai_mapper
masai_output_pe
masai_output_se
mason
micro_razers
pair_align
rabema_build_gold_standard
rabema_evaluate
rabema_prepare_sam
razers
razers3
sak
seqan_tcoffee
snp_store
splazers
stellar
tree_recon
[list was sorted and wildcard expanded (masai_*, rabema_*) by
Andreas Tille]
The other binaries could live happily in /usr/bin/seqan. If there is a
collision, one could prefix seqan_ to the binary name.
According to this advise all binary applications are moved to
/usr/lib/seqan/bin and the ones mentioned above symlinked to /usr/bin.
Manpages were created using help2man for the symlinked binaried.
If you set your PATH like
PATH=${PATH}:/usr/lib/seqan/bin
you can call all seqan tools straight from command line with exception
of /usr/lib/seqan/bin/join since there is a /usr/bin/join inside the
coreutils package which will be found first so you need to explicitly
specify the full path.
If there are good reasons to provide any additional binary under /usr/bin
please file a bug report using `reportbug seqan` and let us know about
your preference.
-- Andreas Tille <tille@debian.org> Wed, 27 Nov 2013 10:26:17 +0100
Note: some apps are not built for some architectures due to memory limitations:
Apps not built for mips & mipsel:
- razers
- razers3
- yara
Apps not built for armhf:
- yara
Apps not built for sh4:
- yara
- razers3
Apps not built for armel:
- yara
Apps not built for kfreebsd-i386:
- yara
Apps not built for hurd-i386:
- yara
Apps not built for ia64:
- searchjoin (assembler errors)
Sending patches to improve the build experience on any of these architectures
would be welcome by the Debian-Med team and upstream.
-- Michael R. Crusoe <michael.crusoe@gmail.com> Fri, 03 Nov 2017 09:29:40 -0700
|
