Closed alpapan closed 7 years ago
alpapan
commented
7 years ago got it.... It seems this happens if there is NO tool that uses type=modules...
Not sure if this means I should close the issue or somehow improve the error message eg
<requirement type="modules">
mvdbeek
commented
7 years ago got it.... It seems this happens if there is NO tool that uses type=modules...
No, that is not right. Please read the introduction in https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html and then https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html#environment-modules-dependency-resolver.
If then you still encounter problems please include the relevant sections of your dependency_resolvers_conf.xml file.
alpapan
commented
7 years ago Hello They were included in the issue above
<modules modulecmd="/usr/bin/modulecmd" modulepath="/data_storage/sysadmin/modules" versionless="true" prefetch="true" find_by="avail"/>Did you modify tools to state <requirement type="modules"> ? This must always be package, not modules.
alpapan
commented
7 years ago Hello It is my own tool so it is not in a shed. I had it as modules because one of the galaxy docs said so.
changed it to package. i assume the it checks using the resolvers until it finds one? (the rest of the dependency file is as default).
by the way, the environment_modules_mapping.yml.sample is empty (and there is no environment_modules_mapping.yml)
will test tomorrow
alpapan
commented
7 years ago 'ModuleDependency' object has no attribute 'name'
nsoranzo
commented
7 years ago I had it as modules because one of the galaxy docs said so.
@alpapan If you can tell us which doc, we can fix it.
alpapan
commented
7 years ago Hello
Sorry I can't find the documentation at the moment.
However I do get the error and I just understand where it may be coming from....:
AttributeError: 'ModuleDependency' object has no attribute 'name'Here is the tool XML that when included causes the above error (and when removed, it also removes the error).
planemo check
$ planemo lint --fail_level error
Linting tool /data_storage/www-cluster/galaxy/tools/alexiesoft_dew2/alexiesoft_dew.xml
Applying linter tests... WARNING
.. WARNING: No tests found, most tools should define test cases.
.. WARNING: No valid test(s) found.
Applying linter output... CHECK
.. INFO: 1 outputs found.
Applying linter inputs... CHECK
.. INFO: Found 10 input parameters.
Applying linter help... CHECK
.. CHECK: Tool contains help section.
.. CHECK: Help contains valid reStructuredText.
Applying linter general... CHECK
.. CHECK: Tool defines a version [21Apr16].
.. CHECK: Tool defines a name [DEW].
.. CHECK: Tool defines an id [alexiesoft_dew].
.. CHECK: Tool specifies profile version [17.05].
Applying linter command... CHECK
.. INFO: Tool contains a command.
Applying linter citations... WARNING
.. WARNING: No citations found, consider adding citations to your tool.
Applying linter tool_xsd... CHECK
.. INFO: File validates against XML schema.Macro:
<macros>
<token name="@VERSION@">21Apr16</token>
<xml name="requirements">
<requirements>
<requirement type="package" version="@VERSION@">DEW</requirement>
</requirements>
</xml>
<xml name="stdio">
<stdio>
</stdio>
</xml>
</macros>Tool's xml (with some code replaced with [....] to reduce it)
<tool id="alexiesoft_dew" name="DEW" version="21Apr16" profile="17.05">
<description>One button differential gene expression with DEW</description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements" />
<expand macro="stdio" />
<command><![CDATA[
#set $read_1_final_list = " "
dew.pl
-infile $reference_genes
-sequence $sequence
-format $select_format
#set $read_1_original_names = " "
#set $uid_path = " "
#for $read_1 in $read_1_list
#set $read_1_final_list += str($read_1) + " "
#set $read_1_original_names += str($read_1.name) + " "
#end for
-1read $read_1_final_list
-uid current
-do_galaxy_cleanup
-sample_names $read_1_original_names
#if $settings.advanced == "a"
$settings.no_graphs
$settings.contextual
$settings.isoforms
$settings.genomewide
#end if
]]></command>
<inputs>
[......]
</inputs>
<outputs>
[....]
</outputs>
<help><![CDATA[
This tools estimates gene expression from any FASTA file
]]></help>
</tool>There is also a temporary .shed.yml but not sure if you want that.
The Dependency XML is now
<dependency_resolvers>
<tool_shed_packages />
<galaxy_packages />
<conda />
<galaxy_packages versionless="true" />
<conda versionless="true" />
<modules modulecmd="/usr/bin/modulecmd" modulepath="/data_storage/sysadmin/modules" versionless="true" prefetch="true" find_by="avail"/>
</dependency_resolvers>Note that my module is a function but i'm using modulecmd= the actual file
$ type module
module is a function
module ()
{
eval `/usr/bin/modulecmd sh $*`
}
$ uname -a
Linux hill 4.4.0-93-generic #116~14.04.1-Ubuntu SMP Mon Aug 14 16:07:05 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
$ module --version
VERSION=3.2.10
DATE=2012-12-21
[...]
$ git branch
* release_17.05Any ideas would be appreciated. i'm sure i'm doing something simple wrong
Hello
I can't seem to find documentation on how to get the environment modules setup correctly. Not sure where ModuleDependency is defined. Error below (after resolving #4452). Any ideas?
XML is
And galaxy release_17.05 is used