- galaxy-dev - lists.galaxyproject.org

shed tool dependencies
by Geert Vandeweyer 14 Feb '14

14 Feb '14

Hi, Is there a default notation to specify perl modules (threading modules) in a tool configuration or in a submission to the toolshed? I've got some tools to share that make extensive use of these modules, and they are not default in a perl distribution. Hence, I'd like to inform the users that they need to install these modules (or that they get installed by the the toolshed using cpan ?) Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/pub/geert-vandeweyer/26/457/726

4 3

external user authentication
by Shrum, Donald C 14 Feb '14

14 Feb '14

I'm having some difficulty with external user authentication as described here - https://wiki.galaxyproject.org/Admin/Config/ExternalUserDatbases I've added these two lines to universe_wsgi.ini use_remote_user = True remote_user_maildomain = fsu.edu I've setup ldap authentication in Apache and verified I have a value in REMOTE_USER with a simple php script... RequestHeader set REMOTE_USER %{AUTHENTICATE_uid}e This adds - REMOTE_USER: dcshrum When I add in the rewrites and forward to galaxy on port 8080 I'm still getting: Access to Galaxy is denied Galaxy is configured to authenticate users via an external method (such as HTTP authentication in Apache), but a username was not provided by the upstream (proxy) server..... Any help debugging this would be greatly appreciated. I'm running out of places to look! --Donny FSU Research Computing Center

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nginx upload
by Briand, Sheldon 14 Feb '14

14 Feb '14

Hi, I'm trying to debug file uploads using the file browser. I have nginx setup to proxy but not to a sub directory. /usr/sbin/nginx -V nginx version: nginx/1.4.3 --add-module=/usr/local/src/nginx_upload_module-2.2.0 Here are the settings in my universe_wsgi.ini: nginx_upload_store = database/tmp/upload_store nginx_upload_path = /_upload Here is the nginx config: user galaxy; worker_processes 1; events { worker_connections 1024; } http { include /etc/nginx/mime.types; default_type application/octet-stream; gzip on; gzip_http_version 1.1; gzip_vary on; gzip_comp_level 4; gzip_proxied any; gzip_types text/plain text/css application/x-javascript text/xml applicatio$ gzip_buffers 16 8k; gzip_disable "MSIE [1-6].(?!.*SV1)"; upstream galaxy_app { server localhost:8080; } log_format main '$remote_addr - $remote_user [$time_local] "$request" ' '$status $body_bytes_sent "$http_referer" ' '"$http_user_agent" "$http_x_forwarded_for"'; access_log /var/log/nginx/access.log main; sendfile on; keepalive_timeout 65; server { listen 80; server_name localhost eugene.imb.nrc.ca; client_max_body_size 10G; #charset koi8-r; #access_log /var/log/nginx/log/host.access.log main; location / { proxy_pass http://galaxy_app; proxy_set_header X-Forwarded-Host $host; proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for; } location /static { alias /software/packages/galaxy/galaxy-dist/static; expires 24h; } location /static/style { alias /software/packages/galaxy/galaxy-dist/static/june_2007_style/blue; expires 24h; } location /static/scripts { alias /software/packages/galaxy/galaxy-dist/static/scripts/packed; } location /favicon.ico { alias /software/packages/galaxy/galaxy_dist/static/favicon.ico; } location /robots.txt { alias /software/packages/galaxy/galaxy-dist/static/robots.txt; } location /_x_accel_redirect/ { internal; alias /; } location /_upload { upload_store /software/packages/galaxy/galaxy-dist/database/tmp/upload_store; upload_pass_form_field ""; upload_set_form_field "__${upload_field_name}__is_composite" "true"; upload_set_form_field "__${upload_field_name}__keys" "name path"; upload_set_form_field "${upload_field_name}_name" "$upload_file_name"; upload_set_form_field "${upload_field_name}_path" "$upload_tmp_path"; upload_pass_args on; upload_pass /_upload_done; } location /_upload_done { set $dst /tool_runner/index; if ($args ~ nginx_redir=([^&]+)) { set $dst $1; } rewrite "" $dst; } error_page 500 502 503 504 /50x.html; location = /50x.html { root /usr/share/nginx/html; } The upload store is on a NFS filesystem. There is nothing in the nginx error log. There is nothing in the paster log. I've noticed that files start to be written to the upload store directory but get cut off by a refresh: -----------------------------234101252030936 Content-Disposition: form-data; name="refresh" refresh The upload usually tries again ~10 times, unless manually cutoff earlier, before giving up. The user usually sees that the data is uploading and that message never goes away. I should mention that I have not yet upgraded to the latest release: $ hg summary parent: 11216:c458a0fe1ba8 I also have debug settings on for galaxy. Likely some setting I've messed up. I'd be grateful for a point in the right direction. I've looked through the archives and googled bunch without success. I saw there have been changes to how the upload module works with nginx 1.3.9+. Should I downgrade my nginx if the newer version don't play nicely with galaxy? Thanks, -Sheldon Sheldon Briand NRC Research Computing Support Analyst Research Computing Support / Soutien Informartique a la Recherche Operations, Science Portfolio / Operations, Portefeuil des sciences SSC-NRC / SPC-CNRC Rm 329A, 1411 Oxford Street / Piece 329A, 1411 Rue Oxford Halifax, NS B3H 3Z1 902 426-1677 sheldon.briand(a)ssc-spc.gc.ca

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popup window possible?
by Neil.Burdett＠csiro.au 13 Feb '14

13 Feb '14

Hi, Is it possible to get a popup dialog box to appear for a tool? If so any examples on this please? i.e. the popup may just give a warning or an info message etc... that the user can confirm before proceeding. Or maybe another way to achieve the same thing? Thanks Neil Neil Burdett Software Engineer | The Australian e-Health Research Centre Computational Informatics CSIRO E: Neil.Burdett(a)csiro.au T: 07 3253 3626 Address: Level 5, UQ Health Science Building 901/16 Royal Brisbane and Women's Hospital, Herston, Brisbane, QLD, 4029 www.csiro.au | http://milxview.csiro.au

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setting up Galaxy for torque pbs
by Ketan Maheshwari 13 Feb '14

13 Feb '14

Hi, I am trying to set up Galaxy to interface with a Cray system which runs Torque/PBS. After reading this Galaxy wiki page: https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster#PBS I was able to scramble torque egg with the following command: LIBTORQUE_DIR=/opt/torque/2.4.11/lib/libtorque.so.2 python scripts/scramble.py -e pbs_python I do not fully understand the "parameters and configuration" part in PBS section of the wiki page. Where exactly the "runner" XML snippet with <plugin> and <destinations> should be placed? Also wondering if the snippet will be required for all tools that I want to run on compute nodes or is it a global setting? Can I tell existing tools to use this setup? Another question is, can I configure Galaxy to submit jobs to compute cluster as a mortal user and not an admin of the system? Thanks, -- Ketan

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History panel filters
by Federico Zambelli 12 Feb '14

12 Feb '14

Dear Galaxy devs, I apologize if somebody has already proposed this idea. I think that it would be great to have a filter for the history panel based on name, data type and so on similar to the one on the tools panel. I really feel the need of it when working on histories with many datasets. Federico Zambelli

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migrate_tools error with latest release (hg update release_2014.02.10 )
by Geert Vandeweyer 12 Feb '14

12 Feb '14

Hi, I'm having problems upgrading Galaxy to the latest release. The migrate tools script gives the following error. No handlers could be found for logger "galaxy.tools" Traceback (most recent call last): File "./scripts/migrate_tools/migrate_tools.py", line 21, in <module> app = MigrateToolsApplication( sys.argv[ 1 ] ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/migrate/common.py", line 45, in __init__ self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 66, in __init__ self.load_dependency_relationships() File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 269, in load_dependency_relationships self.add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies( tool_dependency ) File "/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/installed_repository_manager.py", line 147, in add_entry_to_runtime_tool_dependencies_of_installed_tool_dependencies tool_dependency_util.get_runtime_dependent_tool_dependency_tuples( self.app, tool_dependency, status=None ) File "/galaxy/galaxy-dist/lib/tool_shed/util/tool_dependency_util.py", line 323, in get_runtime_dependent_tool_dependency_tuples env_shell_file_path = td.get_env_shell_file_path( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 533, in get_env_shell_file_path installation_directory = self.installation_directory( app ) File "/galaxy/galaxy-dist/lib/galaxy/model/tool_shed_install/__init__.py", line 548, in installation_directory self.tool_shed_repository.owner, AttributeError: 'NoneType' object has no attribute 'owner' Any help on how to resolve this? The 0009_tools.xml content is : <?xml version="1.0"?> <toolshed name="toolshed.g2.bx.psu.edu"> <repository owner="devteam" changeset_revision="96d2e31a3938" name="bowtie2" description="Bowtie2"> <tool id="bowtie2" version="0.2" file="bowtie2_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="a0c8dc671a23" name="ccat" description="Control-based ChIP-seq Analysis Tool"> <tool id="peakcalling_ccat" version="0.0.1" file="ccat_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="7cc64024fe92" name="clustalw" description="ClustalW multiple sequence alignment program for DNA or proteins"> <tool id="clustalw" version="0.1" file="rgClustalw.xml" /> </repository> <repository owner="devteam" changeset_revision="6708501767b6" name="dwt_cor_ava_perclass" description="Compute P-values and Correlation Coefficients for Feature Occurrences"> <tool id="compute_p-values_correlation_coefficients_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVa_perClass.xml" /> </repository> <repository owner="devteam" changeset_revision="0f2eda4ea8dc" name="dwt_cor_avb_all" description="Compute P-values and Correlation Coefficients for Occurrences of Two Set of Features"> <tool id="compute_p-values_correlation_coefficients_featureA_featureB_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_cor_aVb_all.xml" /> </repository> <repository owner="devteam" changeset_revision="0b89b03ad760" name="dwt_ivc_all" description="Compute P-values and Second Moments for Feature Occurrences"> <tool id="compute_p-values_second_moments_feature_occurrences_between_two_datasets_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_IvC_all.xml" /> </repository> <repository owner="devteam" changeset_revision="cb422b6f49d2" name="dwt_var_perclass" description="Compute P-values and Max Variances for Feature Occurrences"> <tool id="compute_p-values_max_variances_feature_occurrences_in_one_dataset_using_discrete_wavelet_transfom" version="1.0.0" file="execute_dwt_var_perClass.xml" /> </repository> <repository owner="devteam" changeset_revision="d56c5d2e1a29" name="dwt_var_perfeature" description="Wavelet variance using Discrete Wavelet Transfoms"> <tool id="dwt_var1" version="1.0.0" file="execute_dwt_var_perFeature.xml" /> </repository> <repository owner="devteam" changeset_revision="7b0708761d05" name="express" description="Quantify the abundances of a set of target sequences from sampled subsequences"> <tool id="express" version="1.1.1" file="express_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="e28c965eeed4" name="fastqc" description="Read QC reports using FastQC"> <tool id="fastqc" version="1.0.0" file="rgFastQC.xml" /> </repository> <repository owner="devteam" changeset_revision="94306bdd58f7" name="fastq_combiner" description="Combine FASTA and QUAL into FASTQ."> <tool id="fastq_combiner" version="1.0.1" file="fastq_combiner.xml" /> </repository> <repository owner="devteam" changeset_revision="30d9ece6c752" name="fastq_filter" description="Filter FASTQ reads by quality score and length"> <tool id="fastq_filter" version="1.0.0" file="fastq_filter.xml" /> </repository> <repository owner="devteam" changeset_revision="1298445c852b" name="fastq_groomer" description="Convert between various FASTQ quality formats."> <tool id="fastq_groomer" version="1.0.4" file="fastq_groomer.xml" /> </repository> <repository owner="devteam" changeset_revision="5d1e9e13e8db" name="fastq_manipulation" description="Manipulate FASTQ reads on various attributes."> <tool id="fastq_manipulation" version="1.0.1" file="fastq_manipulation.xml" /> </repository> <repository owner="devteam" changeset_revision="5a7b5751617b" name="fastq_masker_by_quality" description="FASTQ Masker by quality score"> <tool id="fastq_masker_by_quality" version="1.0.0" file="fastq_masker_by_quality.xml" /> </repository> <repository owner="devteam" changeset_revision="f0949bc49926" name="fastq_paired_end_deinterlacer" description="FASTQ de-interlacer on paired end reads."> <tool id="fastq_paired_end_deinterlacer" version="1.1" file="fastq_paired_end_deinterlacer.xml" /> </repository> <repository owner="devteam" changeset_revision="b89bdf6acb6c" name="fastq_paired_end_interlacer" description="FASTQ interlacer on paired end reads"> <tool id="fastq_paired_end_interlacer" version="1.1" file="fastq_paired_end_interlacer.xml" /> </repository> <repository owner="devteam" changeset_revision="2793d1d765b9" name="fastq_paired_end_joiner" description="FASTQ joiner on paired end reads"> <tool id="fastq_paired_end_joiner" version="1.0.0" file="fastq_paired_end_joiner.xml" /> </repository> <repository owner="devteam" changeset_revision="c549e99026db" name="fastq_paired_end_splitter" description="FASTQ splitter on joined paired end reads"> <tool id="fastq_paired_end_splitter" version="1.0.0" file="fastq_paired_end_splitter.xml" /> </repository> <repository owner="devteam" changeset_revision="9b7b4e0ca9db" name="fastq_stats" description="FASTQ Summary Statistics by column"> <tool id="fastq_stats" version="1.0.0" file="fastq_stats.xml" /> </repository> <repository owner="devteam" changeset_revision="3571553aeb20" name="fastqtofasta" description="FASTQ to FASTA converter"> <tool id="fastq_to_fasta_python" version="1.0.0" file="fastq_to_fasta.xml" /> </repository> <repository owner="devteam" changeset_revision="bc9269529e88" name="fastq_to_tabular" description="FASTQ to Tabular converter"> <tool id="fastq_to_tabular" version="1.1.0" file="fastq_to_tabular.xml" /> </repository> <repository owner="devteam" changeset_revision="0b9feb0ed628" name="fastq_trimmer" description="FASTQ Trimmer by quality"> <tool id="fastq_trimmer" version="1.0.0" file="fastq_trimmer.xml" /> </repository> <repository owner="devteam" changeset_revision="1cdcaf5fc1da" name="fastq_trimmer_by_quality" description="FASTQ Quality Trimmer by sliding window"> <tool id="fastq_quality_trimmer" version="1.0.0" file="fastq_trimmer_by_quality.xml" /> </repository> <repository owner="devteam" changeset_revision="31154ff9f5e1" name="filter_transcripts_via_tracking" description="Filter Combined Transcripts"> <tool id="filter_combined_via_tracking" version="0.1" file="filter_transcripts_via_tracking.xml" /> </repository> <repository owner="devteam" changeset_revision="acf51ff24c7d" name="find_diag_hits" description="Identify sequence reads corresponding to a particular taxonomic group"> <tool id="find_diag_hits" version="1.0.0" file="find_diag_hits.xml" /> </repository> <repository owner="devteam" changeset_revision="33a0e6aca936" name="freebayes_wrapper" description="Call SNPS with Freebayes"> <tool id="freebayes_wrapper" version="0.5.0" file="freebayes.xml" /> </repository> <repository owner="devteam" changeset_revision="7b1b03c4465d" name="gi2taxonomy" description="Fetch taxonomic representation"> <tool id="Fetch Taxonomic Ranks" version="1.1.0" file="gi2taxonomy.xml" /> </repository> <repository owner="devteam" changeset_revision="2cd5ee197ec7" name="gmaj" description="GMAJ Multiple Alignment Viewer"> <tool id="gmaj_1" version="2.0.1" file="GMAJ.xml" /> </repository> <repository owner="devteam" changeset_revision="33e8ed5a4601" name="lca_wrapper" description="Find lowest diagnostic rank"> <tool id="lca1" version="1.0.1" file="lca.xml" /> </repository> <repository owner="devteam" changeset_revision="ae2ec275332a" name="macs" description="Model-based Analysis of ChIP-Seq"> <tool id="peakcalling_macs" version="1.0.1" file="macs_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="8cd5945559b8" name="poisson2test" description="Poisson two-sample test"> <tool id="poisson2test" version="1.0.0" file="poisson2test.xml" /> </repository> <repository owner="devteam" changeset_revision="82a8234e03f2" name="sicer" description="Statistical approach for the Identification of ChIP-Enriched Regions"> <tool id="peakcalling_sicer" version="0.0.1" file="sicer_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="9e2b9ca7f33a" name="t2ps" description="Draw phylogeny"> <tool id="Draw_phylogram" version="1.0.0" file="t2ps_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="592acb9505fc" name="t2t_report" description="Summarize taxonomy"> <tool id="t2t_report" version="1.0.0" file="t2t_report.xml" /> </repository> <repository owner="devteam" changeset_revision="b334cd1095ea" name="tabular_to_fastq" description="Tabular to FASTQ converter"> <tool id="tabular_to_fastq" version="1.0.0" file="tabular_to_fastq.xml" /> </repository> <repository owner="devteam" changeset_revision="1030acbecce6" name="tophat" description="Find splice junctions using RNA-seq data"> <tool id="tophat" version="1.5.0" file="tophat_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="ffa30bedbee3" name="tophat2" description="Gapped-read mapper for RNA-seq data"> <tool id="tophat2" version="0.6" file="tophat2_wrapper.xml" /> </repository> <repository owner="devteam" changeset_revision="b001b50f2009" name="vcf_annotate" description="Annotate a VCF file (dbSNP, hapmap)"> <tool id="vcf_annotate" version="1.0.0" file="annotate.xml" /> </repository> <repository owner="devteam" changeset_revision="76ad0b7865b9" name="vcf_extract" description="Extract reads from a specified region"> <tool id="vcf_extract" version="1.0.0" file="extract.xml" /> </repository> <repository owner="devteam" changeset_revision="da1a6f33b504" name="vcf_filter" description="Filter a VCF file"> <tool id="vcf_filter" version="1.0.0" file="filter.xml" /> </repository> <repository owner="devteam" changeset_revision="9d162bde4113" name="vcf_intersect" description="Generate the intersection of two VCF files"> <tool id="vcf_intersect" version="1.0.0" file="vcf_tools/intersect.xml" /> </repository> <repository owner="devteam" changeset_revision="66253fc0a69b" name="weblogo3" description="Sequence Logo generator for fasta (eg Clustal alignments)"> <tool id="rgweblogo3" version="0.4" file="rgWebLogo3.xml" /> </repository> </toolshed> Best, Geert -- Geert Vandeweyer, Ph.D. Department of Medical Genetics University of Antwerp Prins Boudewijnlaan 43 2650 Edegem Belgium Tel: +32 (0)3 275 97 56 E-mail: geert.vandeweyer(a)ua.ac.be http://ua.ac.be/cognitivegenetics http://www.linkedin.com/in/geertvandeweyer

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Error installing VarScan from Toolshed
by graham etherington (TSL) 12 Feb '14

12 Feb '14

Hi, I’m trying to install VarScan from the Main Toolshed. I’ve tried both the versions available (‘varscan’ from fcaramia and ‘varscan_version_2’ from devteam), but I get the same error each time: File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/install_util.py", line 294, in install_and_build_package_via_fabric fabric_util.install_and_build_package( app, tool_dependency, actions_dict ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 619, in install_and_build_package destination=full_path_to_dir ) File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__ self.gen.throw(type, value, traceback) File "/tsl/services/galaxy/dist/galaxy-dist/eggs/Fabric-1.7.0-py2.6.egg/fabric/context_managers.py", line 142, in _setenv yield File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py", line 309, in install_and_build_package dir = td_common_util.url_download( work_dir, downloaded_filename, url, extract=True ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 434, in url_download archive = CompressedFile( file_path ) File "/tsl/services/galaxy/dist/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py", line 27, in __init__ self.type = self.file_type 'CompressedFile' object has no attribute 'file_type' Can anyone suggest what might be going wrong here? Many thanks, Graham Dr. Graham Etherington Bioinformatics Support Officer, The Sainsbury Laboratory, Norwich Research Park, Norwich NR4 7UH. UK Tel: +44 (0)1603 450601

2 3

cap3 in galaxy
by Keilwagen, Jens 12 Feb '14

12 Feb '14

Hi, I was pointed to CAP3 by a colleague who likes to have it included in our local Galaxy instance. Searching for cap3 in the Galaxy repositories I only found the packages "package_cap3_3" provided by jjohnson: http://toolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?reposit… http://testtoolshed.g2.bx.psu.edu/repository/preview_tools_in_changeset?rep… So here's my question: Is there any Galaxy integration of cap3? Best regards, Jens

1 0

a question regarding galaxy 'workflow'
by ruiwang.sz 12 Feb '14

12 Feb '14

Hi All, A quick question on the indices. Here is the information provided by the sample file: #Your bowtie_indices.loc file should include an entry per line for each #index set you have stored. The "file" in the path does not actually #exist, but it is the prefix for the actual index files. For example: #hg18canon hg18 hg18 Canonical /depot/data2/galaxy/bowtie/hg18/hg18canon #hg18full hg18 hg18 Full /depot/data2/galaxy/bowtie/hg18/hg18full #/orig/path/hg19 hg19 hg19 /depot/data2/galaxy/bowtie/hg19/hg19 #Note that for backwards compatibility with workflows, the unique ID of #an entry must be the path that was in the original loc file, because that #is the value stored in the workflow for that parameter. That is why the #hg19 entry above looks odd. New genomes can be better-looking. What exactly is "path that was in the original loc file"? Where do I find this "original loc file"? Are we using a newer version of loc file now? I got the loc file from the main galaxy server, and I could see things like following: ce5 ce5 C. elegans (WS180): ce5 /galaxy/data/ce5/bowtie_index/ce5 /galaxy/data/ce6/bowtie_index/ce6 ce6 C. elegans (WS190): ce6 /galaxy/data/ce6/bowtie_index/ce6 Why would ce5 and ce6 appear differently? for ce6, seems the "original loc file path" is the same as the "filebasepath"? galGal3canon galGal3 Chicken (Gallus gallus): galGal3 Canonical /galaxy/data/galGal3/galGal3canon/bowtie_index/galGal3canon /galaxy/data/galGal3/bowtie_index/galGal3 galGal3 Chicken (Gallus gallus): galGal3 Full /galaxy/data/galGal3/galGal3full/bowtie_index/galGal3full but as we could see, for this galGal3, the "original loc file path" is different from the "filebasepath". same for mm9: mm9canon mm9 Mouse (Mus musculus): mm9 Canonical /galaxy/data/mm9/mm9canon/bowtie_index/mm9canon mm9female mm9 Mouse (Mus musculus): mm9 Canonical Female /galaxy/data/mm9/mm9female/bowtie_index/mm9female /galaxy/data/mm9/bowtie_index/mm9 mm9 Mouse (Mus musculus): mm9 Full /galaxy/data/mm9/mm9full/bowtie_index/mm9full How did this get determined? My conjecture is that in the older version of galaxy we don't have mm9canon and mm9female, for example, but we had mm9, and the entry was like: mm9 mm9 mm9 /galaxy/data/mm9/bowtie_index/mm9 but now we are using a newer version of galaxy and mm9 genome was placed in /galaxy/data/mm9/mm9full/bowtie_index/mm9full so we need to modify this loc file to add the mapping so that we don't have to modify the older workflow that uses mm9? is it just because data is organized differently? that's why for all the newer genomes we don't have that? I'd appreciate that if someone could please elaborate a bit. Best Regards, Rui

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