[apollo] Failed Jbrowse Install

Discussion:

Shane McCoy

2016-10-21 18:55:26 UTC

Hello!
Using Apollo 2.0.4
Grails Version: 3.2.1
Groovy Version: 2.4.7
JVM Version: 1.8.0_91

I had a very similar problem previously (not installing Git before) and but
now I do have git installed (used to grab apollo).

*Running ./apollo deploy*

Cloning: https://github.com/gmod/jbrowse into jbrowse-download.

using bower to install: gmod/jbrowse#1.12.2-apollo
/usr/bin/env: ânodeâ: No such file or directory
:installJBrowse FAILED
FAILURE: Build failed with an exception.
Build file '/home/bjreadin/Apollo/build.gradle' line: 326
Execution failed for task ':installJBrowse'.

Process 'command 'bower'' finished with non-zero exit value 127

Run with --stacktrace option to get the stack trace. Run with --info or
--debu option to get more log output.
BUILD FAILED

*Using ./install_jbrowse.sh *

Installing Perl prerequisites ... failed. See setup.log (etc)

*Setup.log*

+ chmod +x web-app/jbrowse/bin/cpanm
chmod: cannot access 'web-app/jbrowse/bin/cpanm': No such file or directory
+ cd web-app/jbrowse
./install_jbrowse.sh: line 26: cd: web-app/jbrowse: No such file or
directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 27: bin/cpanm: No such file or directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 28: bin/cpanm: No such file or directory
+ set -e
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 30: bin/cpanm: No such file or directory

I do have cpanm installed - I used to install all the prereqs. I did use
the --sudo at the end of each module install. could this be a permission
issue?

Thanks,
Shane M.

Shane McCoy

2016-10-21 19:26:57 UTC

Permalink

On a side note - I did try to install JBrowse-1.21.1 on its own and it was
successful.

Post by Shane McCoy
Hello!
Using Apollo 2.0.4
Grails Version: 3.2.1
Groovy Version: 2.4.7
JVM Version: 1.8.0_91
I had a very similar problem previously (not installing Git before) and
but now I do have git installed (used to grab apollo).
*Running ./apollo deploy*
Cloning: https://github.com/gmod/jbrowse into jbrowse-download.

Process 'command 'bower'' finished with non-zero exit value 127

Run with --stacktrace option to get the stack trace. Run with --info or
--debu option to get more log output.
BUILD FAILED

*Using ./install_jbrowse.sh *

Installing Perl prerequisites ... failed. See setup.log (etc)

*Setup.log*

I do have cpanm installed - I used to install all the prereqs. I did use
the --sudo at the end of each module install. could this be a permission
issue?
Thanks,
Shane M.

Nathan Dunn

2016-10-21 19:57:42 UTC

Permalink

Shane. There are a couple of problems that I can see, though I feel as though it should have given you better error feedback.

1 - You need to install the most current and stable version of node / npm. This is new in 2.0.4.

2 - You should either install grails 2.5.5 and load it into your shell (using a tool like sdkman), or uninstall grails altogether and it will load the correct version automatically.

3 - After 1 and 2 are installed, do an ./apollo clean-all and then ./apollo deploy again

Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

On a side note - I did try to install JBrowse-1.21.1 on its own and it was successful.
Hello!
Using Apollo 2.0.4
Grails Version: 3.2.1
Groovy Version: 2.4.7
JVM Version: 1.8.0_91
I had a very similar problem previously (not installing Git before) and but now I do have git installed (used to grab apollo).
Running ./apollo deploy
Cloning: https://github.com/gmod/jbrowse <https://github.com/gmod/jbrowse> into jbrowse-download.
using bower to install: gmod/jbrowse#1.12.2-apollo
/usr/bin/env: ânodeâ: No such file or directory
:installJBrowse FAILED
FAILURE: Build failed with an exception.
Build file '/home/bjreadin/Apollo/build.gradle' line: 326
Execution failed for task ':installJBrowse'.

Process 'command 'bower'' finished with non-zero exit value 127

Run with --stacktrace option to get the stack trace. Run with --info or --debu option to get more log output.
BUILD FAILED
Using ./install_jbrowse.sh
Installing Perl prerequisites ... failed. See setup.log (etc)
Setup.log
+ chmod +x web-app/jbrowse/bin/cpanm
chmod: cannot access 'web-app/jbrowse/bin/cpanm': No such file or directory
+ cd web-app/jbrowse
./install_jbrowse.sh: line 26: cd: web-app/jbrowse: No such file or directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 27: bin/cpanm: No such file or directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 28: bin/cpanm: No such file or directory
+ set -e
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 30: bin/cpanm: No such file or directory
I do have cpanm installed - I used to install all the prereqs. I did use the --sudo at the end of each module install. could this be a permission issue?
Thanks,
Shane M.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

Shane McCoy

2016-10-21 20:35:07 UTC

Permalink

Thanks Nathan!
Correcting both did the trick and I have a successful build and war file.
Many thanks!
Shane M.

Post by Nathan Dunn
Shane. There are a couple of problems that I can see, though I feel as
though it should have given you better error feedback.
1 - You need to install the most current and stable version of node / npm.
This is new in 2.0.4.
2 - You should either install grails 2.5.5 and load it into your shell
(using a tool like sdkman), or uninstall grails altogether and it will load
the correct version automatically.
3 - After 1 and 2 are installed, do an ./apollo clean-all and then ./apollo deploy again
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory
On a side note - I did try to install JBrowse-1.21.1 on its own and it was successful.

Process 'command 'bower'' finished with non-zero exit value 127

Run with --stacktrace option to get the stack trace. Run with --info or
--debu option to get more log output.
BUILD FAILED

*Using ./install_jbrowse.sh *

Installing Perl prerequisites ... failed. See setup.log (etc)

*Setup.log*

+ chmod +x web-app/jbrowse/bin/cpanm
chmod: cannot access 'web-app/jbrowse/bin/cpanm': No such file or directory
+ cd web-app/jbrowse
./install_jbrowse.sh: line 26: cd: web-app/jbrowse: No such file or directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 27: bin/cpanm: No such file or directory
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 28: bin/cpanm: No such file or directory
+ set -e
+ bin/cpanm -v --notest -l ../../extlib/ --installdeps .
./install_jbrowse.sh: line 30: bin/cpanm: No such file or directory

I do have cpanm installed - I used to install all the prereqs. I did use
the --sudo at the end of each module install. could this be a permission
issue?
Thanks,
Shane M.

This list is for the Apollo Annotation Editing Tool. Info at
http://genomearchitect.org/
If you wish to unsubscribe from the Apollo List: 1. From the address with
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Nathan Dunn

2016-10-21 20:58:19 UTC

Permalink

Excellent. Glad it worked out.

Nathan

Post by Shane McCoy
Thanks Nathan!
Correcting both did the trick and I have a successful build and war file.
Many thanks!
Shane M.
Shane. There are a couple of problems that I can see, though I feel as though it should have given you better error feedback.
1 - You need to install the most current and stable version of node / npm. This is new in 2.0.4.
2 - You should either install grails 2.5.5 and load it into your shell (using a tool like sdkman), or uninstall grails altogether and it will load the correct version automatically.
3 - After 1 and 2 are installed, do an ./apollo clean-all and then ./apollo deploy again
Nathan Dunn, PhD
Berkeley Bioinformatics Open-source Projects (BBOP)
Genomics Division, Lawrence Berkeley National Laboratory

Process 'command 'bower'' finished with non-zero exit value 127

This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/ <http://genomearchitect.org/>
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/