error while installing the beta

sequenceserver
#1

Hi,

I get an error while executing sudo gem install --pre sequenceserver

ERROR: While executing gem … (Gem::package::PatheError)
installing into parent path /var/lib/gems/2.3.0/gems/vendor/npm/font-awsome@4.4.0/fonts/FontAwsome.otf of /var/lib/gems/2.3.0/gems/sequenceserver-1.1.0.beta10 is not allowed

Anyone know what this is?
What to do?

Thanks,

Nick

#2

Hi Nick,

I might know what the problem is, but to be sure I need to know what is your operating system. Are you installing on Bash on Windows by any chance?

Priyam

#3

Hi Priyam,

I use linux mint.
Nick

#4

Hi Nick,

There are a few soft links in our gem package. It looks like RubyGems is not able to recreate these soft links during installation. But I am surprised that this would be a problem on a Linux distribution. Could you run "df -Th” and let me know what filesystem do you have (second column)?

It is in my todo list to remove soft links from the gem package. I will do that for the next beta release (which should hopefully be this week) and that will hopefully fix your problem. Alternatively, you could try running directly from git:

git clone https://github.com/wurmlab/sequenceserver
cd sequenceserver
sudo gem install bundler
bundle install --without=development

bundle exec bin/sequenceserver

Priyam

#5

Hi Priyam,

Apparently something worked with your suggestions. See below.
I had the latest blast installed. But 1.1.0.beta10 did not liked it and it downloaded an older version.

On the website there are a lot of databases visible. Many are the same:

#6

using the beta version (see above) I get no blast hits using the nt database.

using the older - stable- version I do get many hits.

Something is not right.

#7

Something has changed. -evalue 1e-5 is applied to all searches. Previous version used BLAST’s default evalue of 10. Could that be the reason you are seeing no hits?

Priyam

#8

Correct. Using -evalue 10 solved the issue. I get similar results
between the two versions.

Any idea what has happened with the multiple database entries in the list?

#9

Can you share a list of files in your database directory? Then I may be able to guess what’s going on with the list of databases in the search form.

#10

Hi Nick,

I just pushed a new release and was wondering if you are now able to install sequenceserver without any errors (gem install --pre sequenceserver).

Priyam

#11

Hi Priyam,

Thanks for the update. Here is the output of the commands:

gem install --pre sequenceserver
Fetching: sequenceserver-1.1.0.beta11.gem (100%)
ERROR: While executing gem ... (Gem::FilePermissionError)
    You don't have write permissions for the /var/lib/gems/2.3.0 directory.
nick@Sylvia-blast ~ $
nick@Sylvia-blast ~ $
nick@Sylvia-blast ~ $ sudo gem install --pre sequenceserver
[sudo] password for nick:
Fetching: sequenceserver-1.1.0.beta11.gem (100%)

#12

Further investigation:
I tried to find configuration files. There is a ~/.sequenceserver
subdirectory with job outputs. I could only find outputs from the non
beta version. The beta version does not create outputs in this
directory.

#13

Hi Nick,

Thanks for confirming that the gem install problem is now resolved. I will get back on multiple database issue as soon as I can.

You can set default options to be applied for running BLAST searches through the config file, which is located at ~/.sequenceserver.conf. To use BLAST’s defaults add the following to your config file:

To use BLAST’s defaults, add:

:options:
blastn: [’-evalue 10 -task megablast’]
blastp: [’-evalue 10’]
blastx: [’-evalue 10’]
tblastn: [’-evalue 10’]
tblastx: [’-evalue 10’]

or if you only want to change for blastn:

:options:
blastn: [’-evalue 10 -task megablast’]

Job data (input and the output) are written to the directory ~/.sequenceserver. BLAST+ binaries and taxdb are also downloaded to ~/.sequenceserver.

Priyam

#14

Hi Nick,

Thanks for being patient. I just pushed a fix for the multiple database issue to GitHub.

I am planning to do a new release only next week, but you can update using git instead of gem:

cd /path/to/sequenceserver
git pull origin master
bundle exec bin/sequenceserver

Priyam