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Bpipe - a tool for running and managing bioinformatics pipelines
Hi, When using bpipe on aws-batch I'm getting the following error ` java.lang.reflect.InvocationTargetException at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62) at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43) at java.base/java.lang.reflect.Method.invoke(Method.java:566) at org.codehaus.groovy.tools.GroovyStarter.rootLoader(GroovyStarter.java:110) at org.codehaus.groovy.tools.GroovyStarter.main(GroovyStarter.java:128) Caused by: java.lang.ExceptionInInitializerError at...
Hi, I get an error running bpipe on an M1 Mac. bpipe version: 0.9.11 installed either manually or from bioconda Is it possible to run bpipe on osx-arm64 architecture? Thanks...
Running trivy against version 0.9.1 reports 25 critical vulnerabilities in dependent libraries used by bpipe. For example: - CVE-2017-17485 [https://avd.aquasec.com/nvd/cve-2017-17485](https://avd.aquasec.com/nvd/cve-2017-17485) - CVE-2016-6809 [https://avd.aquasec.com/nvd/cve-2016-6809]( https://avd.aquasec.com/nvd/cve-2016-6809) Would it be possible to update...
Hi, I am getting this error while I am running the example file, may you please help me in this, (clinker) akhileshmishra@x86_64-apple-darwin13 Clinker-1.32 % bpipe -p out=/Users/akhileshmishra/Documents/Clinker/Clinker-1.32/run -p caller=$CLINKERDIR/test/caller/bcr_abl1.csv -p...
Often on HPC systems, $HOME is read-only on compute nodes to prevent users from using the non-HPC filesystem for processing data. This causes issues if a submit a "local" bpipe...
When using the shebang support in `bpipe`, i.e. scripts leading with: ``` #!/usr/bin/env bpipe ``` the first output line to the terminal is always `Stripping shebang` ``` Stripping shebang ====================================================================================================...
Hi Bpipies, At the moment, when using containered execution (e.g. `singularity`), it is possible to bind extra paths to make them visible inside the container, using a filesystems declaration block....
Hello and thank you for developping Bpipe, it is very useful to me. Would Bpipe be able to execute some steps only if some conditions are met? As an example,...
My pipe file saves as hello.pipe in path of "~/test" and it looks : ` hello = { exec "echo a > a.txt; echo Hello | cat $input.txt - >...
I'm trying to move my variables defined at the top of pipeline into a config file so I can offer differently configured versions. At first glance, I expected to be...