ximmer
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ssadedin
Ximmer is a system for CNV calling on exome and targeted genomic sequencing
For reasons that I don't quite understand, HGFA currently needs to be set in the `eval/config.groovy` in the installation directory (or by setting XIMMER_REF env variable, which then writes to...
This allows curl to follow 302 redirects (especially useful for sourceforge urls for conifer and bwa). Without this, the source for these packages don't end up getting downloaded. Alternatively, could...
This is the error: ``` java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.lang.reflect.Method.invoke(Method.java:498) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:109) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:131) Caused by: org.codehaus.groovy.control.MultipleCompilationErrorsException: startup failed: script15555797947551577614884.groovy: 87: unable to resolve class...
Hello, Only Singularity is installed on our research cluster, not Docker. I have run the Docker container through singularity. When running analysis, I get the following error at the end:...
Hi I've got a new error; the program spits out multiple errors like the one below: ------------------------------------- run_exome_depth ( 8 ) -------------------------------------- Command in stage run_exome_depth failed with exit status...
You have instructions to build the Docker container, but I'd like to convert it into a Singularity container. The easiest way to do this would involve the Docker container living...
Hi I use ximmer in singularity because our HPC do not support docker. Here is one error. How to solve it? Thanks ----------- $ singularity exec ximmer.simg ximmer -v -c...
This is a suggestion. We have a docker platform that users can use the following input to run tools via docker image: input data files: (e.g,: *.bam, ref.fa, taget_region.bed) cmd:...
Hi @ssadedin, I'm trying to to run ximmer on 8 bam files following the guidelines from the website. For 6 I know the gender, for 2 the gender is unknown....
The code in the line `316` of `cnv_diagram.js` is as following: ``` yield { start: pos, end: i, state: newState }; ``` It should be changed to: ``` yield {...
