[jkbonfield]

Ok so first of all, I realise this was a mistake and it's been correct already for the next release - gap5 and gap4 both use the same file extensions, but for completely different file formats. (Or more precisely it's the same underlying mini-database code - hence the matching filenames - but the data that is stored is incompatible.) In the future I'll be using .g5d and .g5x for gap5 database names, with backwards compatibility of course.

So in short, gap4 cannot open the gap5 database. However in Gap5 you should be able to export it in CAF format and then use caf2gap to generate a gap4 database from that. See http://www.sanger.ac.uk/resources/software/caf/

For me if I break a contig in two I then get two smaller contigs. For a while I think it would sometimes split the data in two, but not correctly update the contig start/end locations so it appeared you have two large contigs (while scrolling around would show the data has actually been split). That bug has been fixed already, but maybe that was after the last release.

[alig]

breaking contig in gap5

Hi,

Okay, I can't seem to successfully break a contig in gap5, & I cannot open my .aux file in gap4 to break a contig and search for unpadded positions.

I tried to break a contig in gap5 by putting the base position & it seemed to just duplicate my original contig so I had 2 contigs of the same length!

Is it possible to open my .aux file in gap4? I converted it from an ace file using tg_index

Thanks

alig

[alig]

Searching unpadded position in Gap5

Hi James,

That's a shame, but I imagine it's not an easy task.

Unfortunately my contig is the length of the X chromosome. But I am only interested in a small interval at the beginning so I'll try to break the contig & open in Gap4 to find the unpadded positions.

thanks for your quick reply

alig

[jkbonfield]

I would like to search for unpadded positions in gap5 as none of my variant positions match up in gap5 as the search position box within edit contig view includes pads.

How do I search for an unpadded position in gap5?

Unfortunately right now this isn't possible. I know it's a serious omission and one that I did start to resolve, although that particular solution was driving me stircrazy and I backed out. I do have other plans to address it though. (It's a *lot* harder to implement than it first appears - due to gap5 being an editor rather than just a viewer the mapping of padded to unpadded coordinates is fluid.)

How large are your contigs? The Gap4 approach to this problem is just to compute a consensus and count the number of pads in it, however that's slow on large data.

My apologies for that.

[alig]

how search for unpadded positions in gap5

Hi,

I would like to search for unpadded positions in gap5 as none of my variant positions match up in gap5 as the search position box within edit contig view includes pads.

How do I search for an unpadded position in gap5?

Thanks

alig

[alig]

installing gap5

Hi,
Thank you for pointing me in all the right directions. I got confused and did make install after configure.
All good now, looking forward to using gap5
cheers alig

[jkbonfield]

Did the initial "make" work without errors? It looks like it's missing one of the things it should have just built.

Note that "make install" here doesn't automatically test whether the software have been fully built, and rebuild it if not (unlike many packages).

[alig]

tk_utils Error when make gap5

Hi James,

Thank you for your quick response. I installed the dev package for staden io_lib using synaptic package manager. I now have a different error.

make install
mkdir -p /usr/local/lib/staden
mkdir -p /usr/local/bin
mkdir -p /usr/local/share/staden/etc
mkdir -p /usr/local/share/staden
mkdir -p /usr/local/share/staden/scripts
mkdir -p /usr/local/share/staden/tcl
mkdir -p /usr/local/share/doc
mkdir -p /usr/local/share/man
cp shlib.conf /usr/local/share/staden/etc
cp ../staden.profile /usr/local/share/staden
make JOB=install
make[1]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux'
cd Misc && make -f /usr/local/staden-2.0.0b7-src/build.linux/../Misc/Makefile -w BUILD=/usr/local/staden-2.0.0b7-src/build.linux SRC=/usr/local/staden-2.0.0b7-src/build.linux/../Misc SUBDIR=Misc install
make[2]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux/Misc'
cp /usr/local/staden-2.0.0b7-src/build.linux/lib/libmisc.so /usr/local/lib/staden
make[2]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/Misc'
cd tk_utils && make -f /usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/Makefile -w BUILD=/usr/local/staden-2.0.0b7-src/build.linux SRC=/usr/local/staden-2.0.0b7-src/build.linux/../tk_utils SUBDIR=tk_utils install
make[2]: Entering directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
cp /usr/local/staden-2.0.0b7-src/build.linux/lib/libtk_utils.so /usr/local/lib/staden
cp: cannot stat `/usr/local/staden-2.0.0b7-src/build.linux/lib/libtk_utils.so': No such file or directory
make[2]: *** [install] Error 1
make[2]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
make[1]: *** [tk_utils] Error 2
make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux'
make: *** [install] Error 2

I have tried putting STADENROOT in my .bashrc file, but hasn't helped.

STADENROOT=/usr/local/staden-2.0.0b7-src
export STADENROOT

Any guidance would be greatly received

alig

[jkbonfield]

Hi,

I still cannot launch gap5 & really want to get on & use the program to view my Next Gen data.

When I type ./gap5 to launch it I still get
couldn't read file "/usr/local/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory

I'm also now getting an error when I run make

/usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/misc.c:6:30: error: io_lib/traceType.h: No such file or directory
make[1]: *** [misc.o] Error 1
make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
make: *** [tk_utils] Error 2

Can anyone help me please

alig

So there are two problems here. The first seems to be implying you're compiling it and then attempting to run in situ. You need to run configure with a --prefix option (or let it default to, umm, somewhere - probably /usr/local) and then do a "make install" after compiling. This will copy the compiled bits and tcl files out of the source tree and place them into a directory. Granted I should probably add something to allow running directly out of the build directory as it'd help me a lot too.

The second issue, with io_lib, is less clear. Did you install the staden io_lib library somewhere? Was this by compiling it yourself or by using some prepackaged distribution (eg via synaptic or yum)? If the latter, it's possible that you installed the binaries/libraries but not the development package that contains the header files (eg "io_lib/traceType.h" in this case). The configure script ought to spot this though - I'll investigate.

Finally, I've been reacting to the many issues people have with linking against samtools and iwidgets libraries and have now managed to rewrite the bits of code that depend on these. The next release should therefore have far fewer dependencies and be easier to build. The subversion (svn) copy has these features already if you want to try the bleeding edge release.

James

[alig]

tk_utils Error when make gap5

Hi,

I still cannot launch gap5 & really want to get on & use the program to view my Next Gen data.

When I type ./gap5 to launch it I still get
couldn't read file "/usr/local/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory

I'm also now getting an error when I run make

/usr/local/staden-2.0.0b7-src/build.linux/../tk_utils/misc.c:6:30: error: io_lib/traceType.h: No such file or directory
make[1]: *** [misc.o] Error 1
make[1]: Leaving directory `/usr/local/staden-2.0.0b7-src/build.linux/tk_utils'
make: *** [tk_utils] Error 2

Can anyone help me please

alig

[alig]

problems lauching gap5 and installing manual

Hi,
sorry me again.
I get the following message when try to launch gap5
couldn't read file "/home/neuro/Documents/Gap5/staden-2.0.0b7-src/gap5/../share/staden/tcl/gap5/gap.tcl": no such file or directory
Have tried to set STADENROOT in .bashrc file but doesn't help

Also cannot install gap5 manual as get following error when make unix

! Font \circle=lcircle10 not loadable: Metric (TFM) file not found.
<to be read again>
\allocationnumber
\alloc@ ...ifnum \count 1#1 < #4\allocationnumber
=\count 1#1 \global \advan...
l.5802 \newdimen\circthick

?
! Emergency stop.
<to be read again>
\allocationnumber
\alloc@ ...ifnum \count 1#1 < #4\allocationnumber
=\count 1#1 \global \advan...
l.5802 \newdimen\circthick

No pages of output.
Transcript written on txiversion.log.

kpathsea: Running mktextfm lcircle10
/usr/share/texmf/web2c/mktexnam: Could not map source abbreviation for lcircle10.
/usr/share/texmf/web2c/mktexnam: Need to update ?
mktextfm: Running mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input lcircle10
This is METAFONT, Version 2.718281 (TeX Live 2009/Debian)

kpathsea: Running mktexmf lcircle10

! I can't find file `lcircle10'.
<*> ...jfour; mag:=1; nonstopmode; input lcircle10

Please type another input file name
! Emergency stop.
<*> ...jfour; mag:=1; nonstopmode; input lcircle10

Transcript written on mfput.log.
grep: lcircle10.log: No such file or directory
mktextfm: `mf-nowin -progname=mf \mode:=ljfour; mag:=1; nonstopmode; input lcircle10' failed to make lcircle10.tfm.
kpathsea: Appending font creation commands to missfont.log.
/usr/bin/texi2dvi: texinfo.tex appears to be broken, quitting.
make[1]: *** [manual.pdf] Error 1
rm manual.texinfo
make[1]: Leaving directory `/home/neuro/Documents/Gap5/staden_doc-2.0.0b1-src/manual'
make: *** [common] Error 2

any help gratefully appreciated
alig

[alig]

Re: no functioning samtools when configuring gap5

Hi James,

Thank you very much for your quick reply. I had an earlier version of samtools which didn't have a Makefile to edit.
After downloading samtools-0.1.8 & editing the Makefile by adding -fPIC, then using --with-samtools=DIR with configure, it finds a functioning samtools.

Thanks a bunch, looking forward to using Gap5

alig

[jkbonfield]

It's... complicated!

The problem here is that samtools doesn't have an official make install target, so people who do install it tend to just copy over the binary to <some_package_root>/bin/samtools. We can try and specify that root via --with-samtools, but I need more than just the binary - infact I don't need the binary at all! Then there's the issue about include files. Do people bother to actually install them (normally not). If so, where? Eg should "sam.h" should be included via #include <sam.h>, #include <samtools/sam.h>, #include <sam/sam.h>, etc.

The only logical conclusion I had with all of this is to not bother installing it at all. Instead unpack samtools, build (with -fPIC, see later), and then point gap5 configure at the samtools source tree where you just did the compilation. It's the only foolproof way of picking up the dependencies until a proper samtools installation mechanism exists.

Regarding compilation, note that Gap5 makes use of the library - libbam.a. However it links this into Gap5 run-time libraries; libgap5.so infact. This is implemented as a Tcl plugin and so is a dynamic library that gets loaded at runtime. On many systems that means all code has to be compiled as "position independent code" so it can be moved around in memory. This is enabled via "-fPIC". Unfortunately samtools does not build using that by default as it's only interest is in created a static binary and library, not a dynamic one.

The easiest way to fix this is to edit the samtools Makefile and add -fPIC to the CFLAGS line (before the # mark as everything after that is a comment).

I suspect this is why the configure script is finding samtools directory but failing to consider it as a valid installation. Sorry it's all so complex.

[sklages]

AFAIR there must be a directory structure like this, e.g.,

samtools/lib samtools/include

and the samtools binary itself must be placed in 'samtools' (not in samtools/bin for example).

You will see this if you look into the configure script.

hth,
Sven

[alig]

No functioning samtools found

Hello,

Is anyone else getting this error when configuring Gap5?

configure: WARNING: No functioning samtools found
configure: WARNING: Gap5/tg_index will have reduced functionality

I've got it to configure with all the other dependent libraries & originally I put --with-samtools=DIR (adding my home directory where I'd installed it) & got the above message.

So then I got synaptic package manager to install samtools but get the same message.

It seems to find samtools, but says that it is not functioning. I can use samtools on my computer so do not understand where I am going wrong.

Can anybody help please?

thanks alig