# HG changeset patch
# User kevyin
# Date 1353634049 18000
# Node ID 2948554ae3d7fef7ab00a99c3ff3a98395a8df83
# Parent 5bb9eb050e575f30afa1b8c987fa80a3af6fa65a
added nmeme option
diff -r 5bb9eb050e57 -r 2948554ae3d7 README
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/README Thu Nov 22 20:27:29 2012 -0500
@@ -0,0 +1,40 @@
+Meme-chip wrapper for Galaxy
+
+=========================================:
+========Installation instructions========:
+=========================================:
+The tool_dependencies.xml can attempt to install meme in a folder specific for this tool.
+(such as bwa_wrappers)
+
+The procedure does NOT download motif databases you will need to download them yourself
+
+Meme-chip assumes the meme tools are in PATH.
+Make sure meme is accessible
+
+
+========Tool data table conf========
+Check the meme_chip_motifs entry is in tool_data_table_conf.xml
+
+========Tool loc file========
+
+Example in tool-data/meme_chip_motifs.loc.sample
+Entries come from the motif_db.csv in the motif database folder
+
+make sure:
+- 3 cols
+- tab delimited
+- paths are correct
+
+There is a script to convert the csv to the loc format here:
+https://bitbucket.org/gvl/meme-chip/src
+After running delete the loc entries with multiple paths eg. All Vertebrates
+
+
+=========================================:
+LICENSE for this wrapper:
+=========================================:
+Kevin Ying
+Garvan Institute: http://www.garvan.org.au
+GVL: https://genome.edu.au/wiki/GVL
+
+http://opensource.org/licenses/mit-license.php
diff -r 5bb9eb050e57 -r 2948554ae3d7 meme_chip_wrapper.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/meme_chip_wrapper.xml Thu Nov 22 20:27:29 2012 -0500
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+
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+ meme
+
+
+ echo "MEME version r4.9.0"
+ meme-chip $input_file -o ${memechip_out.files_path}
+ #for p in str.split($motif_dbs.fields.path,","):
+ -db $p
+ #end for
+
+ #if str( $options_type.options_type_selector ) == 'advanced':
+ #if str( $options_type.bg_type.bg_type_selector) == 'bg_user':
+ -bfile "${ str( $options_type.bg_type.bfile ) }"
+ #end if
+
+ #if str( $options_type.nmeme) != '-1':
+ -nmeme "${ str( $options_type.nmeme ) }"
+ #end if
+
+ #if str( $options_type.ccut ) != '-1':
+ -ccut "${ str( $options_type.ccut ) }"
+ #end if
+
+ #if str( $options_type.time ) != '-1':
+ -time "${ str( $options_type.time ) }"
+ #end if
+
+ -desc "${ str( $options_type.desc ) }"
+
+ #if str( $options_type.meme_mod ) != '':
+ -meme-mod "${ str($options_type.meme_mod) }"
+ #end if
+
+ #if str( $options_type.meme_minw ) != '-1':
+ -meme-minw "${ str($options_type.meme_minw) }"
+ #end if
+
+ #if str( $options_type.meme_maxw ) != '-1':
+ -meme-maxw "${ str($options_type.meme_maxw) }"
+ #end if
+
+ #if str( $options_type.meme_nmotifs ) != '-1':
+ -meme-nmotifs "${ str($options_type.meme_nmotifs) }"
+ #end if
+
+ #if str( $options_type.meme_minsites ) != '-1':
+ -meme-minsites "${ str($options_type.meme_minsites) }"
+ #end if
+
+ #if str( $options_type.meme_maxsites ) != '-1':
+ -meme-maxsites "${ str($options_type.meme_maxsites) }"
+ #end if
+
+ #if $options_type.meme_pal:
+ -meme-pal "${ str($options_type.meme_pal) }"
+ #end if
+
+ #if str( $options_type.dreme_e ) != '-1.0':
+ -dreme-e "${ str($options_type.dreme_e) }"
+ #end if
+
+ #if str( $options_type.dreme_m ) != '-1':
+ -dreme-m "${ str($options_type.dreme_m) }"
+ #end if
+
+ #if str($options_type.centrimo_score) != '-1.0':
+ -centrimo-score "${ str($options_type.centrimo_score) }"
+ #end if
+
+ #if str( $options_type.centrimo_maxreg ) != '-1':
+ -centrimo-maxreg "${ str($options_type.centrimo_maxreg) }"
+ #end if
+
+ #if str( $options_type.centrimo_ethresh ) != '-1.0':
+ -centrimo-ethresh "${ str($options_type.centrimo_ethresh) }"
+ #end if
+
+ #if $options_type.centrimo_noseq:
+ -centrimo-noseq
+ #end if
+
+ #end if
+
+ 2>&1 || echo "Error running MEME."
+
+
+ && cd ${memechip_out.files_path}
+ && zip -rp memechip_out ./
+ && mv memechip_out.zip ${memechip_out}
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+ .. class:: infomark
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+ After the job finishes, save the zip file, unzip and open "index.html"
+
+ The actual meme-chip command is displayed under "Command line summary"
+
+ Defaults:
+ http://meme.nbcr.net/meme/doc/meme-chip.html
+
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diff -r 5bb9eb050e57 -r 2948554ae3d7 tool-data/meme_chip_motifs.loc.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool-data/meme_chip_motifs.loc.sample Thu Nov 22 20:27:29 2012 -0500
@@ -0,0 +1,31 @@
+# value name path
+JASPAR CORE JASPAR CORE /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009.meme
+JASPAR CORE vertebrates JASPAR CORE vertebrates /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_vertebrates.meme
+JASPAR CORE fungi JASPAR CORE fungi /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_fungi.meme
+JASPAR CORE insects JASPAR CORE insects /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_insects.meme
+JASPAR CORE nematodes JASPAR CORE nematodes /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_nematodes.meme
+JASPAR CORE plants JASPAR CORE plants /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_plants.meme
+JASPAR CORE urochordates JASPAR CORE urochordates /home/kevyin/bin/meme/db/motif_databases/JASPAR_CORE_2009_urochordates.meme
+JASPAR PHYLOFACTS JASPAR PHYLOFACTS /home/kevyin/bin/meme/db/motif_databases/JASPAR_PHYLOFACTS_2008.meme
+JASPAR FAM JASPAR FAM /home/kevyin/bin/meme/db/motif_databases/JASPAR_FAM_2008.meme
+JASPAR POLII JASPAR POLII /home/kevyin/bin/meme/db/motif_databases/JASPAR_POLII_2008.meme
+JASPAR CNE JASPAR CNE /home/kevyin/bin/meme/db/motif_databases/JASPAR_CNE_2008.meme
+JASPAR SPLICE JASPAR SPLICE /home/kevyin/bin/meme/db/motif_databases/JASPAR_SPLICE_2008.meme
+UniPROBE/BEEML-PBM (Zhao and Stormo 2011) UniPROBE/BEEML-PBM (Zhao and Stormo 2011) /home/kevyin/bin/meme/db/motif_databases/zhao2011.meme
+Human and Mouse (Jolma2010) Human and Mouse (Jolma2010) /home/kevyin/bin/meme/db/motif_databases/jolma2010.meme
+Human and Mouse (MacIsaac THEME) Human and Mouse (MacIsaac THEME) /home/kevyin/bin/meme/db/motif_databases/macisaac_theme.v1.meme
+Prokaryotes (Prodoric Release 8.9) Prokaryotes (Prodoric Release 8.9) /home/kevyin/bin/meme/db/motif_databases/prodoric.meme
+Prokaryotes (RegTransBase v4) Prokaryotes (RegTransBase v4) /home/kevyin/bin/meme/db/motif_databases/regtransbase.meme
+Drosophila (FLYREG; Bergman & Pollard v2) Drosophila (FLYREG; Bergman & Pollard v2) /home/kevyin/bin/meme/db/motif_databases/flyreg.v2.meme
+Drosophila (DMMPMM; Kulakovskiy et al. 2009) Drosophila (DMMPMM; Kulakovskiy et al. 2009) /home/kevyin/bin/meme/db/motif_databases/dmmpmm2009.meme
+Drosophila (iDMMPMM; Kulakovskiy et al. 2009) Drosophila (iDMMPMM; Kulakovskiy et al. 2009) /home/kevyin/bin/meme/db/motif_databases/idmmpmm2009.meme
+Homeodomains (Berger et al.) Homeodomains (Berger et al.) /home/kevyin/bin/meme/db/motif_databases/homeodomain.meme
+Mouse (UniPROBE) Mouse (UniPROBE) /home/kevyin/bin/meme/db/motif_databases/uniprobe_mouse.meme
+Mouse (Chen2008) Mouse (Chen2008) /home/kevyin/bin/meme/db/motif_databases/chen2008.meme
+ETS factors (Wei et al. 2010) ETS factors (Wei et al. 2010) /home/kevyin/bin/meme/db/motif_databases/wei2010*.meme
+E. coli (DPINTERACT) E. coli (DPINTERACT) /home/kevyin/bin/meme/db/motif_databases/dpinteract.meme
+GLIs and TCF7L2/TCF4 (Hallikas et al. 2006) GLIs and TCF7L2/TCF4 (Hallikas et al. 2006) /home/kevyin/bin/meme/db/motif_databases/hallikas2006.meme
+Worm (UniPROBE) Worm (UniPROBE) /home/kevyin/bin/meme/db/motif_databases/uniprobe_worm.meme
+Malaria (Campbell et al. 2010) Malaria (Campbell et al. 2010) /home/kevyin/bin/meme/db/motif_databases/campbell2010_malaria_pbm.meme
+Yeast (MacIsaac v1) Yeast (MacIsaac v1) /home/kevyin/bin/meme/db/motif_databases/macisaac_yeast.v1.meme
+Yeast (SCPD) Yeast (SCPD) /home/kevyin/bin/meme/db/motif_databases/scpd_matrix.meme
diff -r 5bb9eb050e57 -r 2948554ae3d7 tool_data_table_conf.xml.sample
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_data_table_conf.xml.sample Thu Nov 22 20:27:29 2012 -0500
@@ -0,0 +1,8 @@
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diff -r 5bb9eb050e57 -r 2948554ae3d7 tool_dependencies.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/tool_dependencies.xml Thu Nov 22 20:27:29 2012 -0500
@@ -0,0 +1,19 @@
+
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+ ftp://ftp.ebi.edu.au/pub/software/MEME/r4.9.0/rc5/meme_4.9.0.tar.gz
+ ./configure --prefix=$INSTALL_DIR
+ make
+ make install
+
+ $INSTALL_DIR/bin
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+ Skeleton file for meme install. Does not actually install meme.
+
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+