unexpanded macros

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unexpanded macros

Langhorst, Brad
Hi:
I just installed hisat2 and the data manager from the toolshed ….

Some macros seem not to be expanded when I load the tool in the UI (even across galaxy restarts)
e.g. I see @FTYPE@ instead of fastqsanger

the data manager produces this error:
Fatal error: Exit code 1 ()
Traceback (most recent call last):
  File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 85, in <module>
    main()
  File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 79, in main
    build_hisat_index( data_manager_dict, options, params, sequence_id, sequence_name )
  File "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py", line 41, in build_hisat_index
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
  File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 13] Permission denied

that seems to be a result of a missing execute bit for the binaries in 
tool-deps/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin


Should I file issues, or did my installation go wrong?
Any hints to get this running?

Brad


--
Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs


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Re: unexpanded macros

John Chilton-4
Hey Brad,

  What version of Galaxy are you on? Parameterized macros are pretty
new and will not work on older Galaxies.

-John

On Fri, Dec 4, 2015 at 3:36 AM, Langhorst, Brad <[hidden email]> wrote:

> Hi:
> I just installed hisat2 and the data manager from the toolshed ….
>
> Some macros seem not to be expanded when I load the tool in the UI (even
> across galaxy restarts)
> e.g. I see @FTYPE@ instead of fastqsanger
>
> the data manager produces this error:
>
> Fatal error: Exit code 1 ()
> Traceback (most recent call last):
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 85, in <module>
>     main()
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 79, in main
>     build_hisat_index( data_manager_dict, options, params, sequence_id,
> sequence_name )
>   File
> "/mnt/galaxy/data/galaxy/galaxy-toolshed-tools/toolshed.g2.bx.psu.edu/repos/iuc/data_manager_hisat2_index_builder/98a60a4cfb9a/data_manager_hisat2_index_builder/data_manager/hisat2_index_builder.py",
> line 41, in build_hisat_index
>     proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
>   File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 710,
> in __init__
>     errread, errwrite)
>   File "/mnt/galaxy/data/galaxy/sw/lib/python2.7/subprocess.py", line 1327,
> in _execute_child
>     raise child_exception
> OSError: [Errno 13] Permission denied
>
>
> that seems to be a result of a missing execute bit for the binaries in
>
> tool-deps/hisat/2.0/iuc/package_hisat_2_0/c65f00072e57/bin
>
>
>
> Should I file issues, or did my installation go wrong?
>
> Any hints to get this running?
>
>
> Brad
>
>
>
> --
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
>
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
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Re: unexpanded macros

Langhorst, Brad
Hi:

I’m at release_15.05

Some of this was just wrapper bugs (missing @xxx@) looks like dave already fixed this...
I don’t know about this @FTYPE@ stuff though.


it’s working for me like this:


diff -r 6d4d39720545 hisat2.xml
--- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400
+++ b/hisat2.xml Thu Dec 10 17:07:38 2015 -0500
@@ -193,7 +193,7 @@
                     <option value="R">First Strand (R/RF)</option>
                     <option value="F">Second Strand (F/FR)</option>
                 </param>
-                <param argument="--no-spliced-alignment" name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
+                <param argument="--no-spliced-alignment" name="no_spliced_alignment" type="boolean" truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced alignment" />
                 <param format="gtf" label="GTF file with known splice sites" name="known_splice_gtf" optional="True" type="data" />
                 <param display="radio" label="Transcriptome assembly reporting" name="tma" type="select">
                     <option value="">Use default reporting.</option>
diff -r 6d4d39720545 hisat2_macros.xml
--- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400
+++ b/hisat2_macros.xml Thu Dec 10 17:07:38 2015 -0500
@@ -25,12 +25,12 @@
                 <expand macro="paired_end_conditional" />
             </when>
             <when value="paired">
-                <param format="@FTYPE@" label="Forward reads" multiple="true" name="reads_f" type="data" />
-                <param format="@FTYPE@" label="Reverse reads" multiple="true" name="reads_r" type="data" />
+                <param format="fastqsanger" label="Forward reads" multiple="true" name="reads_f" type="data" />
+                <param format="fastqsanger" label="Reverse reads" multiple="true" name="reads_r" type="data" />
                 <expand macro="paired_end_conditional" />
             </when>
             <when value="single">
-                <param format="@FTYPE@" label="Reads" multiple="true" name="reads" type="data" />
+                <param format="fastqsanger" label="Reads" multiple="true" name="reads" type="data" />
             </when>
         </conditional>
     </xml>
@@ -56,7 +56,7 @@
             ${input_format.paired.paired_end_options.no_discordant}
         #end if
     </token>
-    <token name="strandedness_parameters">
+    <token name="@strandedness_parameters@">
         #if str($spliced_options.spliced_options_selector) == "advanced":
             #if str($spliced_options.rna_strandness).strip() != '':
                 --rna-strandness $spliced_options.rna_strandness

Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs


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Re: unexpanded macros

John Chilton-4
Yeah - those wrappers are not going to work with 15.05. Parameterized
XML macros were added in 15.07 it looks like
(http://galaxy.readthedocs.org/en/master/releases/15.07_announce.html).

-John

On Thu, Dec 10, 2015 at 10:28 PM, Langhorst, Brad <[hidden email]> wrote:

> Hi:
>
> I’m at release_15.05
>
> Some of this was just wrapper bugs (missing @xxx@) looks like dave already
> fixed this...
> I don’t know about this @FTYPE@ stuff though.
>
>
> it’s working for me like this:
>
>
> diff -r 6d4d39720545 hisat2.xml
> --- a/hisat2.xml Sat Oct 10 16:24:47 2015 -0400
> +++ b/hisat2.xml Thu Dec 10 17:07:38 2015 -0500
> @@ -193,7 +193,7 @@
>                      <option value="R">First Strand (R/RF)</option>
>                      <option value="F">Second Strand (F/FR)</option>
>                  </param>
> -                <param argument="--no-spliced-alignment"
> name="ignore_quals" type="boolean" truevalue="--no-spliced-alignment"
> falsevalue="" label="Disable spliced alignment" />
> +                <param argument="--no-spliced-alignment"
> name="no_spliced_alignment" type="boolean"
> truevalue="--no-spliced-alignment" falsevalue="" label="Disable spliced
> alignment" />
>                  <param format="gtf" label="GTF file with known splice
> sites" name="known_splice_gtf" optional="True" type="data" />
>                  <param display="radio" label="Transcriptome assembly
> reporting" name="tma" type="select">
>                      <option value="">Use default reporting.</option>
> diff -r 6d4d39720545 hisat2_macros.xml
> --- a/hisat2_macros.xml Sat Oct 10 16:24:47 2015 -0400
> +++ b/hisat2_macros.xml Thu Dec 10 17:07:38 2015 -0500
> @@ -25,12 +25,12 @@
>                  <expand macro="paired_end_conditional" />
>              </when>
>              <when value="paired">
> -                <param format="@FTYPE@" label="Forward reads"
> multiple="true" name="reads_f" type="data" />
> -                <param format="@FTYPE@" label="Reverse reads"
> multiple="true" name="reads_r" type="data" />
> +                <param format="fastqsanger" label="Forward reads"
> multiple="true" name="reads_f" type="data" />
> +                <param format="fastqsanger" label="Reverse reads"
> multiple="true" name="reads_r" type="data" />
>                  <expand macro="paired_end_conditional" />
>              </when>
>              <when value="single">
> -                <param format="@FTYPE@" label="Reads" multiple="true"
> name="reads" type="data" />
> +                <param format="fastqsanger" label="Reads" multiple="true"
> name="reads" type="data" />
>              </when>
>          </conditional>
>      </xml>
> @@ -56,7 +56,7 @@
>              ${input_format.paired.paired_end_options.no_discordant}
>          #end if
>      </token>
> -    <token name="strandedness_parameters">
> +    <token name="@strandedness_parameters@">
>          #if str($spliced_options.spliced_options_selector) == "advanced":
>              #if str($spliced_options.rna_strandness).strip() != '':
>                  --rna-strandness $spliced_options.rna_strandness
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
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Re: unexpanded macros

Langhorst, Brad
Hi John:

I wonder if galaxy tools need a minimum galaxy version flag to avoid 
people trying to install tools that wont work…

probably not worth implementing, but maybe somebody else has a different idea about this.



Brad

Brad Langhorst, Ph.D.
Development Scientist
New England Biolabs


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Re: unexpanded macros

John Chilton-4
Indeed, Galaxy does need that for sure. Eric has created an issue and
I think Dan has some work in progress.

https://github.com/galaxyproject/galaxy/issues/1188

-John

On Thu, Dec 10, 2015 at 10:37 PM, Langhorst, Brad <[hidden email]> wrote:

> Hi John:
>
> I wonder if galaxy tools need a minimum galaxy version flag to avoid
> people trying to install tools that wont work…
>
> probably not worth implementing, but maybe somebody else has a different
> idea about this.
>
>
>
> Brad
> —
> Brad Langhorst, Ph.D.
> Development Scientist
> New England Biolabs
>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/