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<http://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<http://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<http://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
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 <Langhorst@neb.com> 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
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Hi: I’m at release_15.05 Some of this was just wrapper bugs (missing @xxx@) looks like dave already fixed this<https://github.com/nebiolabs/tools-iuc/commit/c07682dc096113a4eb1da10a061cfbee6e769474>... 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
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 <Langhorst@neb.com> 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
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
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 <Langhorst@neb.com> 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
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Langhorst, Brad