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gmms's Introduction

GMMs

A manually curated database of human gut metabolic modules, based on extensive literature review, as described in Vieira-Silva et al. 2016

Format

Module reactions are listed following their order in the module. Tab-separated reactions indicate alternative reactions (OR operation), while return- and comma-separated reactions are all required for process completeness (AND operation).

Mapping

For mapping metagenomic profiles onto the GMMs database please refer to our reference pathways mapper Omixer-RPM.

License

Academic Non-commercial Software License Agreement

Related publications and versioning

For the Vieira-Silva et al. 2016 paper, we used version 1.07 (8cf60cc735) of this repository.

gmms's People

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Forkers

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gmms's Issues

log4j:ERROR Could not parse url [jar:file:/gmms.jar!/lib/BSB-Utils-1.0-alpha-1-SNAPSHOT.jar!/log4j.xml]. java.nio.file.NoSuchFileException: \gmms.jar

”F:\CRC\GMMs-1.0.7\GMMs-1.0.7>java -jar gmms.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/jdmp-0.1.1.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/aspectjweaver-1.6.12.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/javax.inject-1.jar
log4j:ERROR Could not parse url [jar:file:/gmms.jar!/lib/BSB-Utils-1.0-alpha-1-SNAPSHOT.jar!/log4j.xml].
java.nio.file.NoSuchFileException: \gmms.jar“
The above error occurs when I use the above command. What is the reason?

Running problem

Hello,

I can't run your app.
I have an error with log4j, the beginning of error message is :

JarClassLoader: Warning: Null manifest from input stream associated with: lib/jdmp-0.1.1.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/aspectjweaver-1.6.12.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/javax.inject-1.jar
log4j:ERROR Could not parse url [jar:file:/gmms.jar!/lib/BSB-Utils-1.0-alpha-1-SNAPSHOT.jar!/log4j.xml].
java.io.FileNotFoundException: /gmms.jar (No such file or directory)

And my command line is :

java -jar gmms.jar 1 median GMMs.v1.07.txt ../input/ ../output/

I would appreciate your help.
Thanks.

Aurélie

Running problem

Hello,

I can't run your app.
I have an error with log4j, the beginning of error message is :

JarClassLoader: Warning: Null manifest from input stream associated with: lib/jdmp-0.1.1.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/aspectjweaver-1.6.12.jar
JarClassLoader: Warning: Null manifest from input stream associated with: lib/javax.inject-1.jar
log4j:ERROR Could not parse url [jar:file:///Users/joshg/Downloads/test_jar/gmms.jar!/lib/BSB-Utils-1.0-alpha-1-SNAPSHOT.jar!/log4j.xml].
java.io.FileNotFoundException: JAR entry lib/BSB-Utils-1.0-alpha-1-SNAPSHOT.jar!/log4j.xml not found in /Users/joshg/Downloads/test_jar/gmms.jar

And my command line is :

java -jar //Users/joshg/Downloads/test_jar/gmms.jar

I would appreciate your help.
Thanks.

Josh

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