sudo apt-get install sbcl cl-quicklisp make gcc
cd /usr/share/cl-quicklisp
sbcl --load quicklisp.lisp
Kozo Nishida kozo2
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| from pymongo.collection import Collection | |
| client = MongoClient() | |
| db = client['keggscape'] | |
| targets = db['all_target_ids_all'] | |
| ecoli_targets = targets.find({"Species" : "Escherichia coli"}) | |
| convtable = db['conv-eco-uniprot'] |
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| package bar; | |
| import java.io.File; | |
| import java.io.FileInputStream; | |
| import java.io.FileNotFoundException; | |
| import java.io.FileWriter; | |
| import java.io.IOException; | |
| import java.util.Set; | |
| import org.biopax.paxtools.io.BioPAXIOHandler; |
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| sudo su | |
| apt-get install docker.io | |
| cd | |
| mkdir gentoo | |
| cd gentoo | |
| wget http://ftp.jaist.ac.jp/pub/Linux/Gentoo/releases/amd64/current-iso/stage3-amd64-20140403.tar.bz2 | |
| tar jxpf stage3-amd64-20140403.tar.bz2 | |
| tar -c . | docker.io import - gentoo | |
| docker.io run -t -i gentoo /bin/bash |
kozo2
/ start-gentwoo-docker.sh
Last active
August 29, 2015 14:00
getting started - gentwoo (with gentoo docker container)
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| emerge-webrsync | |
| eselect news read new | |
| emerge mirrorselect | |
| mirrorselect -i -o >> /etc/portage/make.conf | |
| mirrorselect -i -r -o >> /etc/portage/make.conf | |
| emerge layman | |
| echo "source /var/lib/layman/make.conf" >> /etc/portage/make.conf | |
| layman -L | |
| layman -a betagarden | |
| CONFIG_PROTECT_MASK="/etc" emerge gentwoo --autounmask-write |
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| ~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level3.owl l3.sbgn | |
| 6014 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371. null | |
| 6015 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax- |
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| ~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level2.owl l2.sbgn | |
| 4942 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 2.2 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction41985 property: DELTA-G) | |
| 4957 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 3.1 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction33853 property: DELTA-G) | |
| 4985 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 11.9 (element: http://biocyc.org/biopax/biopax-level2biochemicalReaction33446 property: DELTA-G) | |
| 4987 [main] WARN org.biopax.paxtools.io.SimpleIOHandler - Binding org.biopax.paxtools.util.IllegalBioPAXArgumentException: Illegal or Dangling Value/Reference: 11 |
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| keymap.replaceKey( "Apps", "RWin" ) | |
| keymap.replaceKey( "Space", "LCtrl" ) | |
| keymap.replaceKey( "Caps", "Enter" ) | |
| keymap.replaceKey( 28, "RAlt" ) | |
| keymap.replaceKey( 29, "LShift" ) | |
| keymap_global[ "O-LCtrl" ] = "Space" | |
| keymap_global[ "S-LCtrl" ] = "S-Space" |
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| brew install hub lein | |
| hub clone daviddpark/drugbank | |
| cd drugbank | |
| lein deps | |
| lein repl |
kozo2
/ gist:a346cd43710d9ef0ab6c
Created
May 21, 2014 15:15
from BioPAX Level3 to SBGN (after removing some tags)
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| ~% java -Xmx4g -jar paxtools-4.2.1.jar toSbgn 18.0/data/biopax-level3.owl l3.sbgn | |
| 5363 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371 to bean http://biocyc.org/biopax/biopax-level3ProteinReference83487; bean class: class org.biopax.paxtools.impl.level3.ProteinReferenceImpl; primary set method: public abstract void org.biopax.paxtools.model.level3.EntityReference.addMemberEntityReference(org.biopax.paxtools.model.level3.EntityReference); value class: class org.biopax.paxtools.impl.level3.SmallMoleculeReferenceImpl. Error: org.biopax.paxtools.util.IllegalBioPAXArgumentException: The range restriction is violated; property: memberEntityReference, bean: http://biocyc.org/biopax/biopax-level3ProteinReference83487--> value: http://biocyc.org/biopax/biopax-level3SmallMoleculeReference115371. null | |
| 5364 [main] ERROR org.biopax.paxtools.controller.PropertyEditor - Failed to set value: http://biocyc.org/biopax/biopax- |