ximmer

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In the line `137` of script `cnv_diagram.js`, the code is as following: ``` var maxTextY = Math.max.apply(null, geneTexts.map(l => l.y)) + characterHeight; ``` I changed the code to something like...

pixuenan

Analysis failed - getting JAVA errors:groovy.lang.MissingMethodException: No signature of method: groovy.util.ConfigObject.MOPs()

16

Im running the analysis on 14 BAM files 7 from tumor and 7 from its germline. which is in a /mnt/d/AKU/FTP/BAM/. I rand the following command to test the tool:...

SafinaAr

============================================ matplotlib ============================================ Installing python package via pip: matplotlib Command python setup.py egg_info failed with error code 1 in /tmp/pip_build_root/matplotlib Storing debug log for failure in /root/.pip/pip.log Installing python package...

jchenpku

High false positive number and x-replacement simulation failure

4

Hello, I'm running ximmer on 15 exome samples from 1000G by docker. Here is my config file ``` title="Test Simulation 15 samples" bam_files=[ "/data/wes/run/20181205/02.bam/HG01200/HG01200_recal.bam", ...... ] target_regions="/data/wes/Ref/bed/SeqCap_EZ_Exome_v3_hg19_capture_targets.bed" simulation_type='downsample' known_cnvs="/data/wes/cnv/00.simulation/15sample_cnv.tsv" samples...

pixuenan

Canot get ximmer to run on Ubuntu 16.04

7

I have been trying (and failing) to run ximmer on an Ubuntu 16.04 LTS server for a few days now. I couldn't get the two CNV callers I tried (connifer...

chapplec

parameter to take in count relatedness in data

1

Thank you for this very useful tool! We are running a few tests using xhmm, cn.mops and exomedepth on a cohort consisting of 24 individual samples and 4 related samples....

gybeata

Error

2

Could you throw some light on this error bpipe.PipelineError: Error evaluating script '~/ximmer/eval/pipeline/config.groovy': No such property: HGFA for class: ~/ximmer/eval/pipeline/config.groovy at bpipe.Pipeline$_loadExternalStagesFromPathList_closure14.doCall(Pipeline.groovy:1027) at bpipe.Pipeline.loadExternalStagesFromPathList(Pipeline.groovy:1000) at bpipe.Pipeline.loadExternalStagesFromPaths(Pipeline.groovy:982) at bpipe.Pipeline.loadExternalStagesFromPaths(Pipeline.groovy) at bpipe.Pipeline.load(Pipeline.groovy:1107)...

SamKap-2

To make a proper conversion to Singularity, we can't have anything in home directories. So one of the commits is to install sdkman into `/usr/local` rather than `/root`. The other...

0xaf1f

eg: ``` analyses { test { cnmops_test_1 { ... } } } ``` It causes the caller to be identifed as cnmops_test.1 which creates a mismatch in the code that...

ssadedin

Sometimes it takes a long time to load, but it isn't clear what is going on as the page just stays white / blank. There should be some kind of...

ssadedin