WIP: Update and test fastx-tools #375

bgruening · 2016-05-23T08:28:54Z

This PR also need a new IUC package package_fastx_toolkit_0_0_14.

mvdbeek · 2016-09-17T15:56:05Z

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

    <outputs>
        <data format="png" name="outfile" metadata_source="input" />
    </outputs>
    <tests>
+        <test>


@bgruening unfortunately this test only passes if I set galaxy's conda version to 4.2.7 :(.
Otherwise I'm getting fastx_toolkit==0.0.14-2 instead of -3. See https://travis-ci.org/galaxyproject/tools-devteam/jobs/160679791#L355

Urgs, this offline bug needs to be fixed. This is really killing us.

mvdbeek · 2016-09-18T09:58:01Z

tool_collections/fastx_toolkit/fastx_barcode_splitter/fastx_barcode_splitter.xml

@@ -1,10 +1,14 @@
-<tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
+<tool id="cshl_fastx_barcode_splitter" version="@VERSION@" name="Barcode Splitter">


@lparsons would you mind if I pull in your fastx_barcode_splitter_enhanced tool as a replacement? I think your version is much more useful.

@mvdbeek Not at all. How can I help with it?

The PR has been opened from the test_fastx branch, if you copy over the tool files here and do a PR selecting the test_fastx brach, we can get your version into this PR.

mvdbeek · 2016-11-10T17:24:19Z

Just so I don't forget this: This is stuck until the conda --offline mode is fixed, so that we can use a newer conda in galaxy. 3.19.3 will not install the latest fastx tool version (0.0.14 build 3 or higher) that is needed for tests to pass.

Unfortunately tests are missing

nsoranzo · 2017-01-01T14:30:59Z

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

+    </macros>
+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>


The macro is imported twice.

nsoranzo · 2017-01-01T14:32:03Z

.travis.yml

@@ -2,52 +2,50 @@ sudo: false
 language: python
 python: 2.7

+# This is a big repository so break Travis CI work into 4 CI jobs.


nsoranzo · 2017-01-01T14:34:58Z

tool_collections/fastx_toolkit/fastq_quality_boxplot/fastq_quality_boxplot.xml

+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>
+	<command>


Indentation

nsoranzo · 2017-01-01T14:38:39Z

..._collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml

+    </macros>
+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>


Macro is imported twice.

nsoranzo · 2017-01-01T14:50:50Z

..._collections/fastx_toolkit/fastx_nucleotides_distribution/fastx_nucleotides_distribution.xml

+    <macros>
+        <import>fastx_macros.xml</import>
+    </macros>
+	<command detect_errors="aggressive">fastx_nucleotide_distribution_graph.sh -t '$input.name' -i $input -o $output</command>


Indentation

bgruening · 2017-01-01T15:05:01Z

@nsoranzo what do you say about the conda upgrade?

bgruening · 2017-01-01T15:08:07Z

@mvdbeek urgs, do you have your branch still around? I think I reverted your changes, sorry.

mvdbeek · 2017-01-01T17:23:54Z

yes, i still have them, resolving conflicts now.

-Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa.

bgruening · 2017-01-01T17:59:52Z

Thanks @mvdbeek!

mvdbeek · 2017-01-01T18:02:14Z

Hmm, looks like there's still something wrong with the dependencies, I'll have a look. At the minimum fastq_quality_boxplot appears to miss gnuplot ... how could I have missed that?!

mvdbeek · 2017-01-01T18:02:50Z

And why are the builds passing? Something is weird here :(.

bgruening · 2017-01-01T18:03:52Z

Not sure. Can you rebase against master and maybe update the travis testing yaml.
I was about to upgrade conda to 4.1.x for testing.

mvdbeek · 2017-01-01T18:27:01Z

At the minimum fastq_quality_boxplot appears to miss gnuplot ... how could I have missed that?!

Ahh, slowly things are coming back ... gnuplot is a dependency of fastx_toolkit in the latest build ... which only install with conda > 3

bgruening · 2017-01-01T18:31:38Z

Let's upgrade the travis testing to conda4 ... in the spirit of galaxyproject/galaxy#3378

nsoranzo · 2017-01-01T21:19:44Z

@nsoranzo what do you say about the conda upgrade?

Fine for me!

bgruening · 2017-01-01T23:28:07Z

@mvdbeek @nsoranzo done in b5efccb

nsoranzo · 2017-01-02T12:41:54Z

@mvdbeek I'm not sure I agree with 70695e1, shouldn't be necessary. The previous Travis build fails because of bioconda/bioconda-recipes#3256 (comment)

mvdbeek · 2017-01-02T12:47:57Z

The previous Travis build fails because of bioconda/bioconda-recipes#3256 (comment)

Yep, but the thing I'm preventing with that commit (which is an alternative version of f1fcf0b) is https://travis-ci.org/galaxyproject/tools-devteam/jobs/188128054#L1131

mvdbeek · 2017-01-02T17:49:08Z

f1fcf0b seems to work for getting planemo back up, but installing planemo within the updated conda env didn't work. I have removed those two commits, but the current situation is not very nice either.

nsoranzo · 2017-01-10T17:08:50Z

.travis.yml

+  - $PLANEMO_CONDA_PREFIX/bin/conda update -y conda
+  - $PLANEMO_CONDA_PREFIX/bin/conda config --get channels # verify conda-forge is not highest priority
+  - $PLANEMO_CONDA_PREFIX/bin/conda config --add channels conda-forge  # moves conda-forge to the top
+  - $PLANEMO_CONDA_PREFIX/bin/conda config --get channels # now conda-forge should be highest priority


conda-forge should have the lowest (not highest) priority, the order (from highest to lowest priority) should be:

iuc

bioconda

r

defaults

conda-forge

and they should be added in reverse order.

yep, I'll have to revert this ... it's being ignored anyway, because planemo use the condarc from ~/.planemo/condarc. Though last time I checked the order was not correct.

If ~/.planemo/condarc is not correct, can we try to overwrite it?

davebx · 2017-07-12T16:30:24Z

tool_collections/fastx_toolkit/fasta_clipping_histogram/fasta_clipping_histogram.xml

@@ -1,18 +1,25 @@
-<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
+<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@VERSION@">


I wonder if this would cause problems, unless the version lineage code recognizes that 0.0.14 > 1.0.0

Oh yes, this is true. Too bad. Are you working on this?

I was planning on moving it to IUC in galaxyproject/tools-iuc#1413, and of course I can merge in your changes there to avoid reinventing effort.

cool, please go ahead and close this when you are ready.

… wrapper versions.

bgruening added the wip label May 23, 2016

mvdbeek mentioned this pull request Sep 15, 2016

Fastx 0.0.14 galaxyproject/tools-iuc#942

Merged

mvdbeek force-pushed the test_fastx branch 2 times, most recently from 5fa2607 to 739dcf1 Compare September 15, 2016 17:16

mvdbeek reviewed Sep 17, 2016

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mvdbeek reviewed Sep 18, 2016

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bgruening mentioned this pull request Dec 17, 2016

fasta_clipping_histogram missing GD/Graph/bars.pm bgruening/docker-galaxy#22

Closed

bgruening added 2 commits January 1, 2017 15:51

Test and update fastx tools

a81f7d5

Upgrade to newer version of fastx

a554313

Unfortunately tests are missing

bgruening force-pushed the test_fastx branch from eab0c77 to a554313 Compare January 1, 2017 14:52

nsoranzo reviewed Jan 1, 2017

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bgruening mentioned this pull request Jan 1, 2017

Use a newer conda version by default galaxyproject/galaxy#3378

Merged

mvdbeek added 9 commits January 1, 2017 18:29

Add tests for the remaining fastx tools

459ff1c

Explicitly set -Q for all non-cs fastq variants

8865acd

-Q 33 is the default, but it needs to be set to -Q 64 for fastqillumina and fastqsolexa.

Close command tag

0c1f99d

Fix command tag ... again

f4e5d27

Fix requirements

f206706

Don't fail with gnuplot warnings

361f286

Use simsize comparison for png

0024992

Retab certain fastx tools, remove duplicate macro imports

3fdc28d

Retab more fastx tools

d55db72

mvdbeek force-pushed the test_fastx branch from 4edd090 to d55db72 Compare January 1, 2017 18:25

mvdbeek force-pushed the test_fastx branch from 3ff1a92 to f1fcf0b Compare January 2, 2017 17:48

mvdbeek mentioned this pull request Jan 3, 2017

Change Conda channel order galaxyproject/galaxy#3237

Merged

nsoranzo reviewed Jan 10, 2017

View reviewed changes

mvdbeek force-pushed the test_fastx branch from e44e6e3 to f1fcf0b Compare January 10, 2017 18:40

Replace '.ext ==' pattern with is_of_type

f9a5168

mvdbeek force-pushed the test_fastx branch from f1fcf0b to f9a5168 Compare January 20, 2017 10:03

martenson mentioned this pull request Jul 10, 2017

Migrate fastx toolkit from tools-devteam, condafy. galaxyproject/tools-iuc#1413

Merged

davebx mentioned this pull request Jul 11, 2017

Apply fixes from upstream git repo. bioconda/bioconda-recipes#5178

Merged

2 tasks

davebx reviewed Jul 12, 2017

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davebx added a commit to davebx/tools-iuc that referenced this pull request Jul 12, 2017

Merge in Björn's changes from galaxyproject/tools-devteam#375, update…

7e2048a

… wrapper versions.

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WIP: Update and test fastx-tools #375

WIP: Update and test fastx-tools #375

bgruening commented May 23, 2016

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		@@ -1,10 +1,14 @@
		<tool id="cshl_fastx_barcode_splitter" version="1.0.0" name="Barcode Splitter">
		<tool id="cshl_fastx_barcode_splitter" version="@VERSION@" name="Barcode Splitter">

		@@ -1,18 +1,25 @@
		<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="1.0.0">
		<tool id="cshl_fasta_clipping_histogram" name="Length Distribution" version="@VERSION@">

WIP: Update and test fastx-tools #375

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WIP: Update and test fastx-tools #375

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