[apollo] prepare-refseqs.pl

Discussion:

[apollo] prepare-refseqs.pl - can't locate

Shane McCoy

2016-10-24 21:43:47 UTC

Hello!
I've run into an issue - would love some help on this one.
After running ./apollo deploy I can't get my head around why the
*bin/prepare-refseqs.pl
<http://prepare-refseqs.pl/>* script is not running

*$ bin/prepare-refseqs.pl <http://prepare-refseqs.pl> --fasta genome.fa

--out /opt/apollo/data*
rc/perl5/../../extlib/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl5/5.22.1
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl
5/x86_64-linux-gnu-thread-multi /home/bjreadin/Apollo/bin/../s
rc/perl5/../../extlib/lib/perl5 /home/bjreadin/Apollo/bin/../src/perl5
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22 /usr/share/perl/5.22
/usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base .) at
/home/bjreadin/Apollo/bin/../src/perl5/JBlibs.pm line 25.
Compilation failed in require at bin/prepare-refseqs.pl line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 5.

Perl Version 5.22.1 - modules installed at:
*/home/bjreadin/perl5/lib/perl5*

I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/src/bioperl-live:/
home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I had no
issues. Could this be due to 5.22.x? Thanks for any insight!
Shane M.

Nathan Dunn

2016-10-24 23:27:57 UTC

Permalink

Shane,

What happens if you run ./install_jbrowse.sh ?

Nathan

Post by Shane McCoy
Hello!
I've run into an issue - would love some help on this one.
After running ./apollo deploy I can't get my head around why the bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> script is not running
$ bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> --fasta genome.fa --out /opt/apollo/data
Compilation failed in require at bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> line 5.
/home/bjreadin/perl5/lib/perl5
I have local::lib installed and my paths seem correct.
$ perl -V
PERL5LIB="/home/bjreadin/src/bioperl-live:/home/bjreadin/perl5/lib/perl5:/home/bjreadin/src/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base
The last perl version I used was 5.18.2 on a previous install and I had no issues. Could this be due to 5.22.x? Thanks for any insight!
Shane M.
This list is for the Apollo Annotation Editing Tool. Info at http://genomearchitect.org/

Shane McCoy

2016-10-25 00:03:17 UTC

Permalink

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not sure if
that matters?

Installing Perl prerequisites ... failed. See setup.log file for error
messages.

Apollo/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

Thanks!
Shane

Shane,
What happens if you run ./install_jbrowse.sh ?
Nathan
Hello!
I've run into an issue - would love some help on this one.
After running ./apollo deploy I can't get my head around why the *bin/prepare-refseqs.pl
<http://prepare-refseqs.pl/>* script is not running
*$ bin/prepare-refseqs.pl <http://prepare-refseqs.pl/> --fasta genome.fa

--out /opt/apollo/data*
rc/perl5/../../extlib/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl5/5.22.1
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl
5/x86_64-linux-gnu-thread-multi /home/bjreadin/Apollo/bin/../s
rc/perl5/../../extlib/lib/perl5 /home/bjreadin/Apollo/bin/../src/perl5
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
.) at /home/bjreadin/Apollo/bin/../src/perl5/JBlibs.pm line 25.
Compilation failed in require at bin/prepare-refseqs.pl line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 5.

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/src/bioperl-live:/home/
bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I had no
issues. Could this be due to 5.22.x? Thanks for any insight!
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
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Shane McCoy

2016-10-25 14:04:09 UTC

Permalink

I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at
/home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm line 64.

I did use --sudo on cpanm installs but I have done that prior without this
issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not sure
if that matters?

Installing Perl prerequisites ... failed. See setup.log file for error
messages.

Apollo/setup.log

Thanks!
Shane

--out /opt/apollo/data*
rc/perl5/../../extlib/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl5/5.22.1
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl
5/x86_64-linux-gnu-thread-multi /home/bjreadin/Apollo/bin/../s
rc/perl5/../../extlib/lib/perl5 /home/bjreadin/Apollo/bin/../src/perl5
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
.) at /home/bjreadin/Apollo/bin/../src/perl5/JBlibs.pm line 25.
Compilation failed in require at bin/prepare-refseqs.pl line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 5.

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I had
no issues. Could this be due to 5.22.x? Thanks for any insight!
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

Deepak Unni

2016-10-25 17:10:00 UTC

Permalink

Hi Shane,

I am stepping in for Nathan as he is busy on a conference this week.

Looking at your recent error with prepare-refseqs.pl script, it looks like
you don't have permission to write to /opt folder.
Since /opt is a system-wide directory, you will have to first create
/opt/apollo as the root user, and then change ownership of /opt/apollo
folder to your username.

Ex:
*sudo mkdir /opt/apollo*
*sudo chown <username>:<group> /opt/apollo*

Once you have this done, you can run the prepare-refseqs.pl script again
and it should process your datasets and place them properly in
/opt/apollo/data.

Let me know if this works or if you encounter any other issues.

Cheers,

Deepak

Post by Shane McCoy
I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at /home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm
line 64.

I did use --sudo on cpanm installs but I have done that prior without this
issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not sure
if that matters?

Installing Perl prerequisites ... failed. See setup.log file for error
messages.

Apollo/setup.log

Thanks!
Shane

--out /opt/apollo/data*
rc/perl5/../../extlib/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl5/5.22.1
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl
5/x86_64-linux-gnu-thread-multi /home/bjreadin/Apollo/bin/../s
rc/perl5/../../extlib/lib/perl5 /home/bjreadin/Apollo/bin/../src/perl5
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
.) at /home/bjreadin/Apollo/bin/../src/perl5/JBlibs.pm line 25.
Compilation failed in require at bin/prepare-refseqs.pl line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 5.

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I had
no issues. Could this be due to 5.22.x? Thanks for any insight!
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

Shane McCoy

2016-10-25 17:12:54 UTC

Permalink

Hi Deepak! thanks for replying. I was just about to send this email when I
saw yours. Here is the updated info:

I have switched to the system perl and added all the proper modules. I
redid my postgresql setup and used the guidelines from the Readdocs

sudo su postgres -c "createuser -RDIElPS $PGUSER"
sudo su postgres -c "createdb -E UTF-8 -O $PGUSER apollo-production"

I updated apollo-config.groovy, plus commented out the password
(didn't do before, missed it!)

ran clean-all and redeployed. Now getting:

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data

Permission denied writing Msax_1-0.txt at /home/bjreadin/Apollo/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 455, <$fasta_fh> line 2.

I can run as sudo now, but I assume that is not the best idea.

Shane

Hi Shane,
I am stepping in for Nathan as he is busy on a conference this week.
Looking at your recent error with prepare-refseqs.pl script, it looks
like you don't have permission to write to /opt folder.
Since /opt is a system-wide directory, you will have to first create
/opt/apollo as the root user, and then change ownership of /opt/apollo
folder to your username.
*sudo mkdir /opt/apollo*
*sudo chown <username>:<group> /opt/apollo*
Once you have this done, you can run the prepare-refseqs.pl script again
and it should process your datasets and place them properly in
/opt/apollo/data.
Let me know if this works or if you encounter any other issues.
Cheers,
Deepak

Post by Shane McCoy
I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at /home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm
line 64.

I did use --sudo on cpanm installs but I have done that prior without
this issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not sure
if that matters?

Installing Perl prerequisites ... failed. See setup.log file for error
messages.

Apollo/setup.log

Thanks!
Shane

genome.fa --out /opt/apollo/data*
rc/perl5/../../extlib/lib/perl5/5.22.1/x86_64-linux-gnu-thread-multi
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl5/5.22.1
/home/bjreadin/Apollo/bin/../src/perl5/../../extlib/lib/perl
5/x86_64-linux-gnu-thread-multi /home/bjreadin/Apollo/bin/../s
rc/perl5/../../extlib/lib/perl5 /home/bjreadin/Apollo/bin/../src/perl5
/etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1 /usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base
.) at /home/bjreadin/Apollo/bin/../src/perl5/JBlibs.pm line 25.
Compilation failed in require at bin/prepare-refseqs.pl line 5.
BEGIN failed--compilation aborted at bin/prepare-refseqs.pl line 5.

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-threa
d-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I had
no issues. Could this be due to 5.22.x? Thanks for any insight!
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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
2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

Deepak Unni

2016-10-25 17:19:54 UTC

Permalink

Hi Shane,

Based on the Permission denied error, it still looks like the script is
having trouble writing to /opt/apollo/data directory.

Running as sudo is not recommended and you might come across additional
errors.

Could you go to /opt/apollo/data folder and try creating a file in that
directory. Chances are you might have Permission Denied.
Let me know if this is the case.

Post by Shane McCoy
Hi Deepak! thanks for replying. I was just about to send this email when I
I have switched to the system perl and added all the proper modules. I
redid my postgresql setup and used the guidelines from the Readdocs
sudo su postgres -c "createuser -RDIElPS $PGUSER"
sudo su postgres -c "createdb -E UTF-8 -O $PGUSER apollo-production"
I updated apollo-config.groovy, plus commented out the password (didn't do before, missed it!)
$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data

Permission denied writing Msax_1-0.txt at /home/bjreadin/Apollo/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 455, <$fasta_fh> line 2.

I can run as sudo now, but I assume that is not the best idea.
Shane

Hi Shane,
I am stepping in for Nathan as he is busy on a conference this week.
Looking at your recent error with prepare-refseqs.pl script, it looks
like you don't have permission to write to /opt folder.
Since /opt is a system-wide directory, you will have to first create
/opt/apollo as the root user, and then change ownership of /opt/apollo
folder to your username.
*sudo mkdir /opt/apollo*
*sudo chown <username>:<group> /opt/apollo*
Once you have this done, you can run the prepare-refseqs.pl script again
and it should process your datasets and place them properly in
/opt/apollo/data.
Let me know if this works or if you encounter any other issues.
Cheers,
Deepak

Post by Shane McCoy
I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at /home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm
line 64.

I did use --sudo on cpanm installs but I have done that prior without
this issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not
sure if that matters?

Installing Perl prerequisites ... failed. See setup.log file for
error messages.

Apollo/setup.log

Thanks!
Shane

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-threa
d-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I
had no issues. Could this be due to 5.22.x? Thanks for any insight!
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.
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with which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

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with which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia

Shane McCoy

2016-10-25 17:24:30 UTC

Permalink

Hi Deepak,
I just got through another redeploy and it is working now. I did chown ...
/opt/apollo/data
thank you for your help!
Shane M.

Post by Deepak Unni
Hi Shane,
Based on the Permission denied error, it still looks like the script is
having trouble writing to /opt/apollo/data directory.
Running as sudo is not recommended and you might come across additional
errors.
Could you go to /opt/apollo/data folder and try creating a file in that
directory. Chances are you might have Permission Denied.
Let me know if this is the case.

Post by Shane McCoy
Hi Deepak! thanks for replying. I was just about to send this email when
I have switched to the system perl and added all the proper modules. I
redid my postgresql setup and used the guidelines from the Readdocs
sudo su postgres -c "createuser -RDIElPS $PGUSER"
sudo su postgres -c "createdb -E UTF-8 -O $PGUSER apollo-production"
I updated apollo-config.groovy, plus commented out the password (didn't do before, missed it!)
$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data

Permission denied writing Msax_1-0.txt at /home/bjreadin/Apollo/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 455, <$fasta_fh> line 2.

I can run as sudo now, but I assume that is not the best idea.
Shane

Hi Shane,
I am stepping in for Nathan as he is busy on a conference this week.
Looking at your recent error with prepare-refseqs.pl script, it looks
like you don't have permission to write to /opt folder.
Since /opt is a system-wide directory, you will have to first create
/opt/apollo as the root user, and then change ownership of /opt/apollo
folder to your username.
*sudo mkdir /opt/apollo*
*sudo chown <username>:<group> /opt/apollo*
Once you have this done, you can run the prepare-refseqs.pl script
again and it should process your datasets and place them properly in
/opt/apollo/data.
Let me know if this works or if you encounter any other issues.
Cheers,
Deepak

Post by Shane McCoy
I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at /home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm
line 64.

I did use --sudo on cpanm installs but I have done that prior without
this issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not
sure if that matters?

Installing Perl prerequisites ... failed. See setup.log file for
error messages.

Apollo/setup.log

Thanks!
Shane

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-threa
d-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I
had no issues. Could this be due to 5.22.x? Thanks for any insight!
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

Deepak Unni

2016-10-25 17:26:26 UTC

Permalink

Awesome! Glad to hear it worked out.

Cheers,

Deepak

Post by Shane McCoy
Hi Deepak,
I just got through another redeploy and it is working now. I did chown ...
/opt/apollo/data
thank you for your help!
Shane M.

Permission denied writing Msax_1-0.txt at /home/bjreadin/Apollo/bin/../src/perl5/Bio/JBrowse/Cmd/FormatSequences.pm line 455, <$fasta_fh> line 2.

I can run as sudo now, but I assume that is not the best idea.
Shane

Hi Shane,
I am stepping in for Nathan as he is busy on a conference this week.
Looking at your recent error with prepare-refseqs.pl script, it looks
like you don't have permission to write to /opt folder.
Since /opt is a system-wide directory, you will have to first create
/opt/apollo as the root user, and then change ownership of /opt/apollo
folder to your username.
*sudo mkdir /opt/apollo*
*sudo chown <username>:<group> /opt/apollo*
Once you have this done, you can run the prepare-refseqs.pl script
again and it should process your datasets and place them properly in
/opt/apollo/data.
Let me know if this works or if you encounter any other issues.
Cheers,
Deepak

Post by Shane McCoy
I am getting permission denied now

$ bin/prepare-refseqs.pl --fasta genome.fa --out /opt/apollo/data
mkdir /opt/apollo: Permission denied at /home/bjreadin/Apollo/bin/../src/perl5/JsonFileStorage.pm
line 64.

I did use --sudo on cpanm installs but I have done that prior without
this issue.

Hi Nathan,

*$ ./install_jbrowse.sh *
Installing Perl prerequisites ...Prerequisites installed, finished.

I had tried after ./apollo clean-all and it would not install. Not
sure if that matters?

Installing Perl prerequisites ... failed. See setup.log file for
error messages.

Apollo/setup.log

Thanks!
Shane

*/home/bjreadin/perl5/lib/perl5*
I have local::lib installed and my paths seem correct.

*$ perl -V*
*/home/bjreadin/perl5/lib/perl5*:/home/bjreadin/sr
c/bioperl-live:/home/bjreadin/perl5/lib"
PERL_LOCAL_LIB_ROOT="/home/bjreadin/perl5:"
PERL_MB_OPT="--install_base "/home/bjreadin/perl5""
PERL_MM_OPT="INSTALL_BASE=/home/bjreadin/perl5"
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib/perl5/5.22.1/x86_64-linux-gnu-threa
d-multi
/home/bjreadin/perl5/lib/perl5/5.22.1
/home/bjreadin/perl5/lib/perl5/x86_64-linux-gnu-thread-multi
*/home/bjreadin/perl5/lib/perl5*
/home/bjreadin/src/bioperl-live
/home/bjreadin/perl5/lib
/etc/perl
/usr/local/lib/x86_64-linux-gnu/perl/5.22.1
/usr/local/share/perl/5.22.1
/usr/lib/x86_64-linux-gnu/perl5/5.22
/usr/share/perl5
/usr/lib/x86_64-linux-gnu/perl/5.22
/usr/share/perl/5.22
/usr/local/lib/site_perl
/usr/lib/x86_64-linux-gnu/perl-base

The last perl version I used was 5.18.2 on a previous install and I
had no issues. Could this be due to 5.22.x? Thanks for any insight!
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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 which you subscribed to the list, send a message to
unsubscribe apollo | 3. Leave the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia
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
| 2. In the subject line of your email type: unsubscribe apollo | 3. Leave
the message body blank.

--
Research Analyst
S104A Animal Science Research Center,
University of Missouri, Columbia