Mercurial > repos > dvanzessen > vep_emc

changeset 6:3333d43a5858 draft

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Uploaded
author dvanzessen
date Tue, 16 Jul 2019 04:57:05 -0400
parents 166e1c2b8c35
children 01748ca044e6
files data_manager/fetch_vep_cache_data.py data_manager/fetch_vep_cache_data.xml data_manager_conf.xml tool-data/vep_cache_data.loc.sample tool_data_table_conf.xml.sample vep.xml
diffstat 6 files changed, 9 insertions(+), 305 deletions(-) [+]
line wrap: on
line diff
--- a/data_manager/fetch_vep_cache_data.py	Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,70 +0,0 @@
-import argparse
-import os
-import json
-import re
-import pprint
-import subprocess
-import sys
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description="Use VEP INSTALL.pl to download/process the cache for an assembly")
-    parser.add_argument("--output-file")
-    parser.add_argument("--output-dir")
-    parser.add_argument("--species")
-    parser.add_argument("--species-type", choices=["ensembl", "refseq", "merged"], default="ensembl")
-    args = parser.parse_args()
-
-    output_file = args.output_file
-    output_dir = args.output_dir
-
-    species = args.species
-    assembly = ""
-    
-    if species.startswith("homo_sapiens"):
-        if species.endswith("37"):
-            assembly = " --ASSEMBLY GRCh37"
-        elif species.endswith("38"):
-            assembly = " --ASSEMBLY GRCh38"
-        else:
-            print("Unknown human assembly")
-            sys.exit(1)
-        species = "homo_sapiens"
-
-    species_type = args.species_type
-    if species_type in ["refseq", "merged"]:
-        species = "{0}_{1}".format(species, species_type)
-    
-    with open(output_file) as output_file_handle:
-        params = json.loads(output_file_handle.read())
-
-    print(output_file)
-    print(output_dir)
-    print(species)
-    print(species_type)
-    pprint.pprint(params)
-
-    if not os.path.exists(output_dir):
-        os.makedirs(output_dir)
-    
-    vep_install_cmd = "vep_install --NO_HTSLIB -a alcf --CACHEDIR {0} --SPECIES {1}{2}".format(output_dir, species, assembly)
-
-    print("Running INSTALL.pl")
-    print(vep_install_cmd)
-    exit_code = subprocess.call(vep_install_cmd, cwd=output_dir, shell=True)
-
-    print(exit_code)
-
-    output_dict = dict(
-        data_tables=dict(
-            vep_cache_data=[{
-                "value": species,
-                "path": output_dir,
-                "dbkey": args.species,
-                "type": species_type,
-                "name": "{0} ({1})".format(args.species, species_type)
-            }]
-        )
-    )
-    with open(output_file, 'w') as output_file_handle:
-        output_file_handle.write(json.dumps(output_dict))
-    sys.exit(exit_code)
\ No newline at end of file
--- a/data_manager/fetch_vep_cache_data.xml	Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,185 +0,0 @@
-<tool id="fetch_vep_cache_data" name="VEP Cache" version="0.0.1" tool_type="manage_data">
-  <requirements>
-    <requirement type="package" version="94.5">ensembl-vep</requirement>
-    <requirement type="package" version="1.642">perl-dbi</requirement>
-    <requirement type="package" version="1.64">perl-archive-zip</requirement>
-    <requirement type="package" version="4.046">perl-dbd-mysql</requirement>
-  </requirements>
-  <description>fetching</description>
-  
-  <command detect_errors="exit_code">
-python $__tool_directory__/fetch_vep_cache_data.py 
---output-file ${ out_file } 
---output-dir ${ out_file.extra_files_path } 
---species ${ species }
---species-type ${ species_type }
-  </command>
-  <inputs>
-    <param name="species" type="select" label="Species">
-      <option value="homo_sapiens37">homo_sapiens (GRCh37)</option>
-      <option value="homo_sapiens38">homo_sapiens (GRCh38)</option>
-      <option value="orycteropus_afer_afer">orycteropus_afer_afer</option>
-      <option value="mus_spretus">mus_spretus</option>
-      <option value="vicugna_pacos">vicugna_pacos</option>
-      <option value="poecilia_formosa">poecilia_formosa</option>
-      <option value="colobus_angolensis_palliatus">colobus_angolensis_palliatus</option>
-      <option value="anolis_carolinensis">anolis_carolinensis</option>
-      <option value="dasypus_novemcinctus">dasypus_novemcinctus</option>
-      <option value="scleropages_formosus">scleropages_formosus</option>
-      <option value="labrus_bergylta">labrus_bergylta</option>
-      <option value="stegastes_partitus">stegastes_partitus</option>
-      <option value="periophthalmus_magnuspinnatus">periophthalmus_magnuspinnatus</option>
-      <option value="rhinopithecus_bieti">rhinopithecus_bieti</option>
-      <option value="saimiri_boliviensis_boliviensis">saimiri_boliviensis_boliviensis</option>
-      <option value="pan_paniscus">pan_paniscus</option>
-      <option value="cavia_aperea">cavia_aperea</option>
-      <option value="melopsittacus_undulatus">melopsittacus_undulatus</option>
-      <option value="haplochromis_burtoni">haplochromis_burtoni</option>
-      <option value="otolemur_garnettii">otolemur_garnettii</option>
-      <option value="ciona_intestinalis">ciona_intestinalis</option>
-      <option value="ciona_savignyi">ciona_savignyi</option>
-      <option value="caenorhabditis_elegans">caenorhabditis_elegans</option>
-      <option value="cebus_capucinus_imitator">cebus_capucinus_imitator</option>
-      <option value="felis_catus">felis_catus</option>
-      <option value="astyanax_mexicanus">astyanax_mexicanus</option>
-      <option value="ictalurus_punctatus">ictalurus_punctatus</option>
-      <option value="gallus_gallus">gallus_gallus</option>
-      <option value="pan_troglodytes">pan_troglodytes</option>
-      <option value="cricetulus_griseus">cricetulus_griseus</option>
-      <option value="pelodiscus_sinensis">pelodiscus_sinensis</option>
-      <option value="anabas_testudineus">anabas_testudineus</option>
-      <option value="amphiprion_ocellaris">amphiprion_ocellaris</option>
-      <option value="gadus_morhua">gadus_morhua</option>
-      <option value="latimeria_chalumnae">latimeria_chalumnae</option>
-      <option value="propithecus_coquereli">propithecus_coquereli</option>
-      <option value="bos_taurus">bos_taurus</option>
-      <option value="macaca_fascicularis">macaca_fascicularis</option>
-      <option value="fukomys_damarensis">fukomys_damarensis</option>
-      <option value="octodon_degus">octodon_degus</option>
-      <option value="canis_lupus_familiaris">canis_lupus_familiaris</option>
-      <option value="tursiops_truncatus">tursiops_truncatus</option>
-      <option value="mandrillus_leucophaeus">mandrillus_leucophaeus</option>
-      <option value="anas_platyrhynchos">anas_platyrhynchos</option>
-      <option value="astatotilapia_calliptera">astatotilapia_calliptera</option>
-      <option value="loxodonta_africana">loxodonta_africana</option>
-      <option value="mustela_putorius_furo">mustela_putorius_furo</option>
-      <option value="ficedula_albicollis">ficedula_albicollis</option>
-      <option value="drosophila_melanogaster">drosophila_melanogaster</option>
-      <option value="takifugu_rubripes">takifugu_rubripes</option>
-      <option value="nomascus_leucogenys">nomascus_leucogenys</option>
-      <option value="capra_hircus">capra_hircus</option>
-      <option value="mesocricetus_auratus">mesocricetus_auratus</option>
-      <option value="rhinopithecus_roxellana">rhinopithecus_roxellana</option>
-      <option value="gorilla_gorilla_gorilla">gorilla_gorilla_gorilla</option>
-      <option value="seriola_dumerili">seriola_dumerili</option>
-      <option value="cavia_porcellus">cavia_porcellus</option>
-      <option value="poecilia_reticulata">poecilia_reticulata</option>
-      <option value="eptatretus_burgeri">eptatretus_burgeri</option>
-      <option value="papio_hamadryas">papio_hamadryas</option>
-      <option value="erinaceus_europaeus">erinaceus_europaeus</option>
-      <option value="equus_caballus">equus_caballus</option>
-      <option value="procavia_capensis">procavia_capensis</option>
-      <option value="oryzias_melastigma">oryzias_melastigma</option>
-      <option value="oryzias_latipes">oryzias_latipes</option>
-      <option value="dipodomys_ordii">dipodomys_ordii</option>
-      <option value="petromyzon_marinus">petromyzon_marinus</option>
-      <option value="panthera_pardus">panthera_pardus</option>
-      <option value="jaculus_jaculus">jaculus_jaculus</option>
-      <option value="echinops_telfairi">echinops_telfairi</option>
-      <option value="chinchilla_lanigera">chinchilla_lanigera</option>
-      <option value="neolamprologus_brichardi">neolamprologus_brichardi</option>
-      <option value="aotus_nancymaae">aotus_nancymaae</option>
-      <option value="macaca_mulatta">macaca_mulatta</option>
-      <option value="kryptolebias_marmoratus">kryptolebias_marmoratus</option>
-      <option value="callithrix_jacchus">callithrix_jacchus</option>
-      <option value="pteropus_vampyrus">pteropus_vampyrus</option>
-      <option value="myotis_lucifugus">myotis_lucifugus</option>
-      <option value="amphilophus_citrinellus">amphilophus_citrinellus</option>
-      <option value="xiphophorus_couchianus">xiphophorus_couchianus</option>
-      <option value="mus_musculus">mus_musculus</option>
-      <option value="mus_musculus_castaneus">mus_musculus_castaneus</option>
-      <option value="microcebus_murinus">microcebus_murinus</option>
-      <option value="mus_musculus_musculus">mus_musculus_musculus</option>
-      <option value="mus_musculus_domesticus">mus_musculus_domesticus</option>
-      <option value="fundulus_heteroclitus">fundulus_heteroclitus</option>
-      <option value="heterocephalus_glaber">heterocephalus_glaber</option>
-      <option value="peromyscus_maniculatus_bairdii">peromyscus_maniculatus_bairdii</option>
-      <option value="esox_lucius">esox_lucius</option>
-      <option value="mola_mola">mola_mola</option>
-      <option value="papio_anubis">papio_anubis</option>
-      <option value="monodelphis_domestica">monodelphis_domestica</option>
-      <option value="amphiprion_percula">amphiprion_percula</option>
-      <option value="pongo_abelii">pongo_abelii</option>
-      <option value="chrysemys_picta_bellii">chrysemys_picta_bellii</option>
-      <option value="ailuropoda_melanoleuca">ailuropoda_melanoleuca</option>
-      <option value="paramormyrops_kingsleyae">paramormyrops_kingsleyae</option>
-      <option value="sus_scrofa">sus_scrofa</option>
-      <option value="sus_scrofa_map">sus_scrofa_map</option>
-      <option value="macaca_nemestrina">macaca_nemestrina</option>
-      <option value="ochotona_princeps">ochotona_princeps</option>
-      <option value="xiphophorus_maculatus">xiphophorus_maculatus</option>
-      <option value="ornithorhynchus_anatinus">ornithorhynchus_anatinus</option>
-      <option value="microtus_ochrogaster">microtus_ochrogaster</option>
-      <option value="pundamilia_nyererei">pundamilia_nyererei</option>
-      <option value="oryctolagus_cuniculus">oryctolagus_cuniculus</option>
-      <option value="rattus_norvegicus">rattus_norvegicus</option>
-      <option value="pygocentrus_nattereri">pygocentrus_nattereri</option>
-      <option value="ceratotherium_simum_simum">ceratotherium_simum_simum</option>
-      <option value="mus_caroli">mus_caroli</option>
-      <option value="saccharomyces_cerevisiae">saccharomyces_cerevisiae</option>
-      <option value="poecilia_latipinna">poecilia_latipinna</option>
-      <option value="ovis_aries">ovis_aries</option>
-      <option value="cyprinodon_variegatus">cyprinodon_variegatus</option>
-      <option value="poecilia_mexicana">poecilia_mexicana</option>
-      <option value="sorex_araneus">sorex_araneus</option>
-      <option value="mus_pahari">mus_pahari</option>
-      <option value="choloepus_hoffmanni">choloepus_hoffmanni</option>
-      <option value="cercocebus_atys">cercocebus_atys</option>
-      <option value="physter_macrocephalus">physter_macrocephalus</option>
-      <option value="acanthochromis_polyacanthus">acanthochromis_polyacanthus</option>
-      <option value="lepisosteus_oculatus">lepisosteus_oculatus</option>
-      <option value="ictidomys_tridecemlineatus">ictidomys_tridecemlineatus</option>
-      <option value="gasterosteus_aculeatus">gasterosteus_aculeatus</option>
-      <option value="monopterus_albus">monopterus_albus</option>
-      <option value="carlito_syrichta">carlito_syrichta</option>
-      <option value="sarcophilus_harrisii">sarcophilus_harrisii</option>
-      <option value="tetraodon_nigroviridis">tetraodon_nigroviridis</option>
-      <option value="panthera_tigris_altaica">panthera_tigris_altaica</option>
-      <option value="hippocampus_comes">hippocampus_comes</option>
-      <option value="oreochromis_niloticus">oreochromis_niloticus</option>
-      <option value="cynoglossus_semilaevis">cynoglossus_semilaevis</option>
-      <option value="tupaia_belangeri">tupaia_belangeri</option>
-      <option value="scophthalmus_maximus">scophthalmus_maximus</option>
-      <option value="meleagris_gallopavo">meleagris_gallopavo</option>
-      <option value="nannospalax_galili">nannospalax_galili</option>
-      <option value="chlorocebus_sabaeus">chlorocebus_sabaeus</option>
-      <option value="notamacropus_eugenii">notamacropus_eugenii</option>
-      <option value="gambusia_affinis">gambusia_affinis</option>
-      <option value="xenopus_tropicalis">xenopus_tropicalis</option>
-      <option value="seriola_lalandi_dorsalis">seriola_lalandi_dorsalis</option>
-      <option value="taeniopygia_guttata">taeniopygia_guttata</option>
-      <option value="maylandia_zebra">maylandia_zebra</option>
-      <option value="danio_rerio">danio_rerio</option>
-      <option value="mastacembelus_armatus">mastacembelus_armatus</option>
-      <option value=""></option>
-    </param>
-    <param name="species_type" type="select" label="Get the Ensembl, Refseq or merged Ensembl/Refseq">
-      <option value="ensembl" selected="true">Ensembl</option>
-      <option value="refseq">Refseq</option>
-      <option value="merged">Merged</option>
-    </param>
-  </inputs>
-  <outputs>
-    <data name="out_file" format="data_manager_json"/>
-  </outputs>
-  <!-- 
-  <tests>
-      <test>
-          DON'T FORGET TO DEFINE SOME TOOL TESTS
-      </test>
-  </tests>
-  -->
-  <help>
-  There is no help
-  </help>
-</tool>
--- a/data_manager_conf.xml	Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,20 +0,0 @@
-<?xml version="1.0"?>
-<data_managers>
-    <data_manager tool_file="data_manager/fetch_vep_cache_data.xml" id="fetch_vep_cache_data">
-            <data_table name="vep_cache_data">
-                <output>
-                    <column name="value" />
-                    <column name="dbkey" />
-                    <column name="type" />
-                    <column name="name" />
-                    <column name="path" output_ref="out_file" >
-                        <move type="directory">
-                            <source>${path}</source>
-                            <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/seq/${path}</target>
-                        </move>
-                        <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/${dbkey}/seq/${path}</value_translation>
-                    </column>
-                </output>
-            </data_table>
-    </data_manager>
-</data_managers>
--- a/tool-data/vep_cache_data.loc.sample	Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-# VEP data cache location
-# <value>   <dbkey>   <type>    <name>    <path>
-# <value> unique key of an entry (species_<type>)
-# <dbkey> galaxy ref key
-# <type> cache type, ensembl, refseq or merged
-# <name> display name of the entry
-# <path> path to the directory of the cache dir
\ No newline at end of file
--- a/tool_data_table_conf.xml.sample	Mon Jul 15 09:37:13 2019 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,7 +0,0 @@
-<?xml version="1.0"?>
-<tables>
-    <table name="vep_cache_data" comment_char="#" allow_duplicate_entries="False">
-        <columns>value, dbkey, type, name, path</columns>
-        <file path="tool-data/vep_cache_data.loc" />
-    </table>
-</tables>
--- a/vep.xml	Mon Jul 15 09:37:13 2019 -0400
+++ b/vep.xml	Tue Jul 16 04:57:05 2019 -0400
@@ -1,19 +1,8 @@
 <tool id="vep" name="Vep" version="0.1.0">
     <requirements>
         <requirement type="package" version="94.5">ensembl-vep</requirement>
-        <requirement type="package" version="1.642">perl-dbi</requirement>
-        <requirement type="package" version="1.64">perl-archive-zip</requirement>
-        <requirement type="package" version="4.046">perl-dbd-mysql</requirement>
     </requirements>
     <command detect_errors="exit_code"><![CDATA[
-        #if str( $species.fields.type ) == "refseq":
-            #set $cache_type = "--refseq"
-        #elif str( $species.fields.type ) == "merged":
-            #set $cache_type = "--merged"
-        #else:
-            #set $cache_type = ""
-        #end if
-
         #if $output_options.cell_type.strip():
             #set $cell_type = '--cell_type ' + str( $output_options.cell_type )
         #else:
@@ -74,9 +63,9 @@
         --no_stats
         --dir_plugins $__tool_directory__/dir_plugins
         --cache
-        --dir_cache ${species.fields.path}
+        --dir_cache /vep_cache
         --force_overwrite
-        --species ${species.fields.dbkey}
+        --species ${species}
         $cache_type
         --input_file "$input" 
         --output_file "$output"
@@ -151,9 +140,13 @@
     <inputs>
         <param type="data" name="input" format="vcf" />
         <param name="species" type="select">
-            <options from_data_table="vep_cache_data">
-                <validator type="no_options" message="Run the data manager to fetch cache data"/>
-            </options>
+            <option value="mus_musculus" selected="true">Mus musculus</option>
+            <option value="homo_sapiens">Homo sapiens</option>
+        </param>
+        <param name="cache_type" type="select">
+            <option value="" selected="true">ensembl</option>
+            <option value="--refseq">refseq</option>
+            <option value="--merged">merged</option>
         </param>
         <param name="offline" type="select">
                 <option value="--offline">Yes</option>