Can't add sff files in gsAssembler and gsMapper v2.7

[guibar]

Hi,

I have managed to install version 2.7 of the roche assembler and mapper on ubuntu 12.04 but I am left with a weird problem.

Everything seems to work except that in the GUI of both applications (gsAssembler and gsMapper), I can't add sff or fasta files to the project. When I click on the + button I get a file selector but after I select a file and click 'ok', nothing happens. Interestingly, in the mapper when I add a reference sequence I don't have this problem even though it looks very similar from an interface point of view.

I have managed to go round this by tweaking the xml file that represents the project and adding the sff files there but it is tedious and I would like to fix this problem.

I am using version 1.6.0_30 of the jre which is the one that comes with the software.

Has anyone seen this?

Thanks

[Torst]

The "Open file" dialogue boxes are strangely different between Linux, Mac and Windows when using the JRE. Sometimes they only allow the selection of a FOLDER, but the same dialog on a different platform expects a FILE. I don't know how to resolve the issue I describe, but it could be related to your issue.

[mbseq]

Has anybody found a solution to this problem? I am having the same issue with Ubuntu and Newbler 2.8. The workaround of editing the .xml file seems to work for gsMapper projects, but the gsAssembler does not even create a project folder.

[sklages]

Here it works just fine 2.7, 2.8, Ubuntu 64bit, my own java,

java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01, mixed mode)

Install your own java 1.6 (not 1.7) and edit the relevant scripts.

hth,
Sven

[JJMS]

Hi,

I have managed to install version 2.7 of the roche assembler and mapper on ubuntu 12.04 but I am left with a weird problem.

Everything seems to work except that in the GUI of both applications (gsAssembler and gsMapper), I can't add sff or fasta files to the project. When I click on the + button I get a file selector but after I select a file and click 'ok', nothing happens. Interestingly, in the mapper when I add a reference sequence I don't have this problem even though it looks very similar from an interface point of view.

I have managed to go round this by tweaking the xml file that represents the project and adding the sff files there but it is tedious and I would like to fix this problem.

I am using version 1.6.0_30 of the jre which is the one that comes with the software.

Has anyone seen this?

Thanks

Had the same problem... Solved it by reinstalling the software with option "Local" instead of "system" somewhere in the beginning of the instalation

[sinnamone]

Same problems

Could help me, i have the same problem, what I have to reinstall?

[sklages]

Could help me, i have the same problem, what I have to reinstall?

The Roche software ..

[yifangt]

could not load file to projects of newbler2.9

Hi Sklages!
I could not add any data to the projects either, either .sff or .fasta/q files!!!, that I met with Newbler2.9.
You seem to be the only one who have experience to solve this problem.
Could you please be more specific with what you did?
Here is my java information

java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1ubuntu0.12.10.2)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)

my kernel:

Linux yt 3.5.0-42-generic #65-Ubuntu SMP Tue Oct 1 23:38:22 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux

Thanks a lot in advance!

[sklages]

How has the Roche software suite been installed? As a local user or system wide?
Which java is used by the Roche software? As the software ships with its own java, your system wide java is not necessarily the one used by Roche.
Check this via e.g.

strace -o output gsAssembler

Look for java in output; it should tell you the path to the java binary used.

But I am the lazy one, I have

- installed the most current 64bit Java 1.6 (not 1.7!) locally
- edited all relevant scripts $ROCHE_SOFTWARE/bin to use this java binary (grep -l JAVA bin/*)
- no sorrows anymore with Roche's software (with respect to java) :-)

hth

[yifangt]

JAVA for newbler2.9

Thanks Sklages!
There is a long list about java from the trace output, such as:

open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_30/bin/../lib/i386/jli/tls/i686/sse2/libpthread.so.0", O_RDONLY) = -1 ENOENT (No such file or directory)
stat64("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_30/bin/../lib/i386/jli/tls/i686/sse2", 0xfffeb500) = -1 ENOENT (No such file or directory)
......

It seems the JAVA for my newbler is

jre1.6.0_30

as I found the line in one app (for example,gsAssembler):

 APP_JRE_HOME="$APP_HOME/../jre/jre1.6.0_30/"

Also when I tried following command

~/download-software/newbler2.9/apps/jre/jre1.6.0_30/bin$ ./java 
Error: no `server' JVM at `/home/yifang/download-software/newbler2.9/apps/jre/jre1.6.0_30/lib/i386/server/libjvm.so'.

Get closer to solve the problem. Any clue with this? Thanks a lot!

yt

[sklages]

I'd go for a separate Java.

- Download and "install" a new 64bit Oracle Java, maybe somewhere in "newbler2.9/java".

- Have a look which files need editing:

cd newbler2.9/bin
grep -w JAVA *

- open the scripts, at the end set your own Java, e.g. gsAssembler

The end of the script, just before the program itself is called, mine looks like this:

## (1) Roche 454 Suite is NOT compatible with Java 7
## -> Install newest Oracle Java 6, 1.6.0_33
export JAVA_HOME="/package/sequencer/Java/6"
export JAVA="$JAVA_HOME"/bin/java

echo "Using package java in $JAVA_HOME"
$JAVA -version
echo ""

# ---------------------------------------------------------------------
# Start
# ---------------------------------------------------------------------
exec "$JAVA" "${finalJavaArgs[@]}" com.simontuffs.onejar.Boot $enableVersion $enableVerbose $*

Set JAVA_HOME accordingly, here "/path/to/newbler2.9/java".
I use my own own java since version 2.3 AFAIR, without any problems. I have used Sun/Oracle Java because of performance issues reported years ago, and I stuck with it ;-)

hth, Sven

[yifangt]

RE: JAVA newbler2.9

Thanks Sven!
I downloaded jre1.6.0.45-x64 from Oracle, which seems to be the newest version of jre1.6.0, and installed it in

~/download-software/newbler2.9/apps/jre/jre1.6.0_45/

beside the Roche jre1.6.0_30 folder.
then I changed the line in the program srcipt gsAssembler (and other programs too.)

APP_JRE_HOME="$APP_HOME/../jre/jre1.6.0_30/"
to
[COLOR="Blue"]APP_JRE_HOME="$APP_HOME/../jre/jre1.6.0_45/"[/COLOR]

then

export JAVA="$APP_JRE_HOME"/bin/java

The problem did not go away.
Can I ask which version of newbler is yours? newbler2.8 or 2.7? As I did not see the those lines in my newbler2.9:

export JAVA_HOME="/package/sequencer/Java/6"
export JAVA="$JAVA_HOME"/bin/java

echo "Using package java in $JAVA_HOME"
$JAVA -version
echo ""

which seems not matter, but I am not sure. Did I miss anything?
I am not familiar with java, not sure jre1.6.0_45 is of problem. Thank you so much for your help.
yt

[yifangt]

And I straced the errors are:

access("/etc/ld.so.preload", R_OK)      = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/tls/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/tls/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/tls/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/tls", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/tls/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/tls/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/tls/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/tls", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../jre/lib/amd64/jli", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/tls/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/tls/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/tls/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/tls", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/tls/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/tls/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/tls/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/tls", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64", {st_mode=S_IFDIR|0755, st_size=4096, ...}) = 0
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/tls/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/tls/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/tls/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/tls", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/x86_64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/x86_64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64/libpthread.so.0", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
stat("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/../lib/amd64", 0x7fff1d010470) = -1 ENOENT (No such file or directory)
open("/etc/ld.so.cache", O_RDONLY|O_CLOEXEC) = 6

open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/libdl.so.2", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)

open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/libc.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
access("/etc/ld.so.nohwcap", F_OK)      = -1 ENOENT (No such file or directory)

open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/bin/../lib/amd64/jli/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/server/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)
open("/home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45/lib/amd64/libm.so.6", O_RDONLY|O_CLOEXEC) = -1 ENOENT (No such file or directory)

Thanks a lot again!
yt

[sklages]

Don't touch the APP vars, there is no need to do so.

Just before the actual call of the java binary at the very end of the script, you can add the lines I posted (with your specific path to java). Then it should work.

That is how my "final section" looks like (complete):

# ---------------------------------------------------------------------
# Before you run the application specify the location of the
# java runtime base directory which will be used for running
# ---------------------------------------------------------------------

# sklages, 2013-08-08 =========================================================

## (1) Roche 454 Suite is NOT compatible with Java 7
## -> Install newest Oracle Java 6, 1.6.0_33
export JAVA_HOME="/package/sequencer/Java/6"
export JAVA="$JAVA_HOME"/bin/java

echo "Using package java in $JAVA_HOME"
$JAVA -version
echo ""

## sklages, 2013-08-08 =========================================================


# ---------------------------------------------------------------------
# Start
# ---------------------------------------------------------------------
exec "$JAVA" "${finalJavaArgs[@]}" com.simontuffs.onejar.Boot $enableVersion $enableVerbose $*

Just copy these lines and replace everything after

# ---------------------------------------------------------------------
# Before you run the application specify the location of the
# java runtime base directory which will be used for running
# ---------------------------------------------------------------------

Currently I use 2.9. But this works for every version (>=2.3).

[yifangt]

Humm, I did exactly as you suggested. When I ran:

/home/yt/download-software/newbler2.9/apps/gsAssembler/bin$ ./gsAssembler

I had message as:

Using package java in /home/yt/download-software/newbler2.9/apps/jre/jre1.6.0_45
java version "1.6.0_45"
Java(TM) SE Runtime Environment (build 1.6.0_45-b06)
Java HotSpot(TM) 64-Bit Server VM (build 20.45-b01, mixed mode)

which seems the new JAVA is running instead of the Roche default one. The newbler GUI is working too, but I still could not add sequence to project menu, which had a warning exclamation mark.
The strace output are the same long list of errors. Strange! I will try more.......
Thank you very much Sven!

Merry Christmas and Happy New Year!