test failed

[nagoue]

Hi, I am testing FROGS on local computer (Ubuntu) and I am facing a basic problem. I cloned the git repository and installed dependencies. At the test step, I got this error:

IOError: [Errno 2] No such file or directory: '/home/Logiciels/galaxy17_05/galaxy/tools/my_tools/FROGS/libexec/preprocess_tpl.html' Error in preprocess Why does it look for the preprocess_tpl.html file in the libexec folder? This file is localized in tools/preprocess folder and the symlink is in the app folder. Should I create a symlink to libexec folder ? This option sounds strange to me... Thank you, Nadia

[mariabernard]

Hello Nadia,

We agree that you clone the master branch of the git repository ?

Correct me if I am wrong, but it seems that you make some links of the python script of each tool in the libexec directory, no ? Normally you do not need to do anything like this.

Just :

• clone the master repository
• in the libexec folder, add links for software used in FROGS : flash, cutadapt, swarm, vsearch, blastn, jar of RDP classifier, RScript ...... (everything in the dependancies section of the README)
• in the tool_conf.xml Galaxy file just add tools by writing path of the FROGS XML files available in the app folder (or simply copy and paste line from the readme)
• in the static/images Galaxy folder, make a link named frogs to the FROGS/img folder.

and this is it.

Does this help ?

[nagoue]

Hi Maria,

I cloned the master branch like this git clone https://github.com/geraldinepascal/FROGS.git I haven't made symlink but just suggesting that could maybe solve my error problem. Dependencies were in my PATH so I changed and made links in the libexec to the required tools.

The error message changed to test.sh: ligne 28: preprocess.py : command not found Error in preprocess

In FROGS/app : preprocess.py -> ../tools/preprocess/preprocess.py* preprocess_tpl.html -> ../tools/preprocess/preprocess_tpl.html preprocess.xml -> ../tools/preprocess/preprocess.xml

In FROGS/tools/preprocess preprocess.py* preprocess_tpl.html preprocess.xml

Sorry, I am not familiar with python. The one installed is python 2.7.13 It looks like an environment issue.

Thank you

[mariabernard]

could you list your libexec directory ? what is the test.sh command line you used ?

[nagoue]

my libexec directory: drwxrwxr-x 2 nagoue nagoue 4096 oct. 10 13:21 ./ drwxrwxr-x 10 nagoue nagoue 4096 oct. 6 11:43 ../ -rwxrwxr-x 1 nagoue nagoue 12133 sept. 27 14:58 addAffiliation2biom.py -rwxrwxr-x 1 nagoue nagoue 10702 sept. 27 14:58 biom2tsv.py -rwxrwxr-x 1 nagoue nagoue 3594 sept. 27 14:58 biomFastaUpdate.py -rwxrwxr-x 1 nagoue nagoue 26717 sept. 27 14:58 biomTools.py lrwxrwxrwx 1 nagoue nagoue 15 oct. 10 11:18 blastn -> /usr/bin/blastn lrwxrwxrwx 1 nagoue nagoue 71 oct. 10 11:22 classifier.jar -> /home/nagoue/Logiciels/miniconda2/share/rdptools-2.0.2-0/classifier.jar lrwxrwxrwx 1 nagoue nagoue 32 oct. 10 11:17 cutadapt -> /home/nagoue/.local/bin/cutadapt -rwxrwxr-x 1 nagoue nagoue 16792 sept. 27 14:58 derepSamples.py -rwxrwxr-x 1 nagoue nagoue 3942 sept. 27 14:58 extractSwarmsFasta.py -rwxrwxr-x 1 nagoue nagoue 9910 sept. 27 14:58 filterSeq.py lrwxrwxrwx 1 nagoue nagoue 20 oct. 10 11:16 flash -> /usr/local/bin/flash -rwxrwxr-x 1 nagoue nagoue 4393 sept. 27 14:58 multiAffiFromBiom.py -rwxrwxr-x 1 nagoue nagoue 28734 sept. 27 14:58 parallelChimera.py -rwxrwxr-x 1 nagoue nagoue 11012 sept. 27 14:58 remove454Adapt.py -rwxrwxr-x 1 nagoue nagoue 12833 sept. 27 14:58 removeConta.py -rwxrwxr-x 1 nagoue nagoue 1401 sept. 27 14:58 root_tree.R -rwxrwxr-x 1 nagoue nagoue 18685 sept. 27 14:58 silva2retrainRDP.py -rwxrwxr-x 1 nagoue nagoue 6525 sept. 27 14:58 sortAbundancies.py -rwxrwxr-x 1 nagoue nagoue 26705 sept. 27 14:58 splitbc.pl lrwxrwxrwx 1 nagoue nagoue 14 oct. 10 11:17 swarm -> /usr/bin/swarm -rwxrwxr-x 1 nagoue nagoue 5329 sept. 27 14:58 swarm2biom.py -rwxrwxr-x 1 nagoue nagoue 14040 sept. 27 14:58 tsv2biom.py lrwxrwxrwx 1 nagoue nagoue 16 oct. 10 11:18 vsearch -> /usr/bin/vsearch

The command I launched is from FROGS/test directory:

$ bash test.sh /home/nagoue/Logiciels/galaxy17_05/galaxy_tools/FROGS/test/ 2 4 /home/nagoue/Documents/results/galaxy/

[mariabernard]

The libexec is ok

But your command line is wrong! Assuming that you clone FROGS in /home/nagoue/Logiciels/galaxy17_05/galaxy_tools/, remove "test/" at the end of your FROGS_PATH

bash test.sh /home/nagoue/Logiciels/galaxy17_05/galaxy_tools/FROGS/ 2 4 /home/nagoue/Documents/results/galaxy/ 

[nagoue]

That's right! but I still have the error message:

Step preprocess mardi 10 octobre 2017, 14:46:10 (UTC+0200) test.sh: ligne 28: preprocess.py : command not found Error in preprocess

[mariabernard]

It should work. We miss something!

Could you:

ls /home/nagoue/Logiciels/galaxy17_05/galaxy_tools/FROGS

and

ls /home/nagoue/Logiciels/galaxy17_05/galaxy_tools/FROGS/app

in my case, in a new session

 
preprocess.py
preprocess.py : commande introuvable

if I execute the first line of the test.sh

frogs_dir=/home/maria/workspace/git/FROGS_master
export PATH=$frogs_dir/libexec:$frogs_dir/app:$PATH
export PYTHONPATH=$frogs_dir/lib:$PYTHONPATH
preprocess.py
usage: preprocess.py [-h] [-v] {illumina,454} ...
preprocess.py: error: too few arguments

it works.

[nagoue]

OK, I found a mistake in my path. Shame on me!! I apologize for your time. Thank you Maria !