Start:
#contents
* General Questions [#s659d678]
*** What GMV can do? [#x5f5faa8]
GMV is a comparative genome browser, to explore the resul...
It can load Murasaki's results, genome sequences and thei...
GMV has several filtering and reporting features, to help...
studies.
*** Can I try GMV (and murasaki) by just downloading the ...
If you're using MacOS X or Microsoft Windows, yes. Please...
Also, Murasaki binary for MacOS X 10.5 is available at [[...
*** Is GMV able to visualize non-Murasaki results from BL...
No. But there are some converter scripts (ex: mauve2ancho...
included in Murasaki's tarball. You may be able to visual...
other tools' results by converting them into ".anchors" a...
format of Murasaki.
*** There are many files in Murasaki's output. Which are ...
GMV requires these files:
- .seqs
- .anchors
- sequence files (.fa, .gbk, etc.)
GMV optionally (and automatically, if exists) reads these...
- .anchors.details
- .stats.tfidf
- .repeats
- sequence length files: (.fa.length, .gbk.length, etc.)
- .ntseqs (tmurasakix generates this)
and GMV may generate:
- .stats.tfidf (if this doesn't exist but .anchors.detail...
- detailed sequence length files: (.fa.len, .gbk.len, etc.)
- .bmk (bookmark)
* Platform specific FAQ [#c02bfdf5]
** MacOS X [#aea22fcb]
*** Is Snow Leopard supported? [#y33b5e23]
Surely. I'm writing the code on Snow Leopard.
The binary distribution works on MacOS X 10.4 (Tiger) and...
and Intel platforms are supported). It works with Quartz...
graphics interface of MacOS X), but It'll be easy to comp...
if you try to compile by yourself.
*** I'm running Panther (or older) MacOS X! [#j832f5c3]
You can compile/run GMV, if you have X11 and GTK+ install...
Mac. But this may need some hacking effort today, because...
longer supports older versions than Tiger.
** Microsoft Windows [#z3ca1811]
*** Which version of Windows are supported? [#gbf3f57c]
GMV works on Windows 2000, XP and Vista.
Running the binary requires [[GTK+ runtime:http://sourcef...
is also possible to build on Cygwin or MinGW/MSYS. The di...
binary is cross-compiled on my Mac with MinGW library.
** Linux [#qee3f19b]
*** Are there are any binary package for Linux? [#w96e63a1]
No... There are too many distributions to maintain the bi...
distribution. Please compile GMV from the source tarball.
** FreeBSD [#p73545aa]
*** Is GMV available in Ports collection? [#d43c9a41]
I want to do that... Anybody want to use it? If so, pleas...
* Building GMV [#c46dfde6]
*** What kind of platforms are supported? [#sd851e7f]
I usually build GMV on:
- MacOS X (10.4 and later, PowerPC and Intel)
- Windows with MinGW
- FreeBSD
and it should be able to compiled on:
- Linux and other Un*x clones
- Cygwin
*** Which version of GTK+ is required? [#zf08a286]
Basically, GMV requires 2.12.x or later (2.10.x may work).
To build with GTK+-Quartz on MacOS X, 2.14.7 seems to be ...
2.16.x is a little bit buggy with Quartz, and I haven't t...
yet.
End:
#contents
* General Questions [#s659d678]
*** What GMV can do? [#x5f5faa8]
GMV is a comparative genome browser, to explore the resul...
It can load Murasaki's results, genome sequences and thei...
GMV has several filtering and reporting features, to help...
studies.
*** Can I try GMV (and murasaki) by just downloading the ...
If you're using MacOS X or Microsoft Windows, yes. Please...
Also, Murasaki binary for MacOS X 10.5 is available at [[...
*** Is GMV able to visualize non-Murasaki results from BL...
No. But there are some converter scripts (ex: mauve2ancho...
included in Murasaki's tarball. You may be able to visual...
other tools' results by converting them into ".anchors" a...
format of Murasaki.
*** There are many files in Murasaki's output. Which are ...
GMV requires these files:
- .seqs
- .anchors
- sequence files (.fa, .gbk, etc.)
GMV optionally (and automatically, if exists) reads these...
- .anchors.details
- .stats.tfidf
- .repeats
- sequence length files: (.fa.length, .gbk.length, etc.)
- .ntseqs (tmurasakix generates this)
and GMV may generate:
- .stats.tfidf (if this doesn't exist but .anchors.detail...
- detailed sequence length files: (.fa.len, .gbk.len, etc.)
- .bmk (bookmark)
* Platform specific FAQ [#c02bfdf5]
** MacOS X [#aea22fcb]
*** Is Snow Leopard supported? [#y33b5e23]
Surely. I'm writing the code on Snow Leopard.
The binary distribution works on MacOS X 10.4 (Tiger) and...
and Intel platforms are supported). It works with Quartz...
graphics interface of MacOS X), but It'll be easy to comp...
if you try to compile by yourself.
*** I'm running Panther (or older) MacOS X! [#j832f5c3]
You can compile/run GMV, if you have X11 and GTK+ install...
Mac. But this may need some hacking effort today, because...
longer supports older versions than Tiger.
** Microsoft Windows [#z3ca1811]
*** Which version of Windows are supported? [#gbf3f57c]
GMV works on Windows 2000, XP and Vista.
Running the binary requires [[GTK+ runtime:http://sourcef...
is also possible to build on Cygwin or MinGW/MSYS. The di...
binary is cross-compiled on my Mac with MinGW library.
** Linux [#qee3f19b]
*** Are there are any binary package for Linux? [#w96e63a1]
No... There are too many distributions to maintain the bi...
distribution. Please compile GMV from the source tarball.
** FreeBSD [#p73545aa]
*** Is GMV available in Ports collection? [#d43c9a41]
I want to do that... Anybody want to use it? If so, pleas...
* Building GMV [#c46dfde6]
*** What kind of platforms are supported? [#sd851e7f]
I usually build GMV on:
- MacOS X (10.4 and later, PowerPC and Intel)
- Windows with MinGW
- FreeBSD
and it should be able to compiled on:
- Linux and other Un*x clones
- Cygwin
*** Which version of GTK+ is required? [#zf08a286]
Basically, GMV requires 2.12.x or later (2.10.x may work).
To build with GTK+-Quartz on MacOS X, 2.14.7 seems to be ...
2.16.x is a little bit buggy with Quartz, and I haven't t...
yet.
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