CWL workflow as Debian package
Hello, I had an exchange with Stian yesterday about what CWL workflow of his database he would propose to use as an experience-gathering example. He proposed the GATK workflow by Farah Zaib Khan et al. for being good to cite about workflows and reproducibility. https://doi.org/10.1186/s12859-017-1747-0 https://github.com/skanwal/GATK-CaseStudy/tree/master/CWL We have BWA, GATK and Picard Toolkit already in Debian from what I understand (not sure about the state of GATK). Stian had pointed to https://github.com/h3abionet/h3agatk/blob/master/workflows/GATK/GATK-complete-WES-Workflow-h3abionet.cwl as a current variant of the same, but then again, I would not mind to start with a smaller one. Any comments? The main point for me is to have a small test case for running this workflow repeatedly. We would hence also need to decide on appropriate test data at some point. Should we also introduce a package like "genome-human"? Best, Steffen
Changes to the imagej package and please update
Hi I am now packaging an ImageJ plugin that uses maven as build system. For that, it makes use of the ij.jar in Maven Central and the related pom.xml file which is part of ImageJA [1]. In addition, the plugin is a Java library on its own right and as such has its javadocs which are dependent on the imagej javadocs which are not currently packaged. I am fixing both of those issues on the debian imagej package but this would be made simpler if the package was updated first. Could you please update it for the latest (1.51p)? No need to actually upload the new version. More details on why: I have asked pkg-java on how to best to handle the issue of the pom.xml and was told to simply download the pom file from ImageJA and include it on the debian directory and then install it with maven-repo-helper. I have accomplished that [2] but had to fudge it because for some reason ImageJA skipped the version 1.51i [3] which is the one currently packaged in Debian. I would prefer not have to fudge anything. I managed to change the imagej package to also build the imagej javadocs and have an extra libimagej-java-docs package for it. However, this currently fails due to a bug on ImageJ which I believed is fixed on later releases. Maybe this is the reason why ImageJA skipped version 1.51i since they also release javadocs. --- Since I would be adding a libimagej-java-doc packages, maybe it would make sense to have the pair libimagej-java? The lib package would just package /use/share/java/ij.jar while the imagej package would have the actual ImageJ program. Carnë [1] http://imagej.net/ImageJA [2] https://github.com/carandraug/debian-imagej/commit/6ef7c9836d22b48 [3] http://maven.imagej.net/content/groups/public/net/imagej/ij/
What's the reason to use legacy minia instead of current version?
Hi, since Nadiya is working on a test for minia I was checking the status. According to the homepage[1] consideres the packaged version 1.6906 legacy code. There are several new releases available at Githib[2]. Is there any good reason to stick with the legacy code rather than packaging the current code? Kind regards Andreas. [1] http://minia.genouest.org/ [2] https://github.com/GATB/minia/releases -- http://fam-tille.de
Re: Changes to the imagej package and please update
Hi Carnë I just run uscan + gbp import-orig and pushed. Feel free to do this yourself in case of the problems you have described below. Or tell me if I missed the point and I should do more. Kind regards Andreas. On Fri, Aug 11, 2017 at 07:32:30PM +0100, Carnë Draug wrote: > Hi > > I am now packaging an ImageJ plugin that uses maven as build system. > For that, it makes use of the ij.jar in Maven Central and the related > pom.xml file which is part of ImageJA [1]. In addition, the plugin is > a Java library on its own right and as such has its javadocs which are > dependent on the imagej javadocs which are not currently packaged. > > I am fixing both of those issues on the debian imagej package but this > would be made simpler if the package was updated first. Could you > please update it for the latest (1.51p)? No need to actually upload > the new version. > > More details on why: > > I have asked pkg-java on how to best to handle the issue of the > pom.xml and was told to simply download the pom file from ImageJA and > include it on the debian directory and then install it with > maven-repo-helper. I have accomplished that [2] but had to fudge it > because for some reason ImageJA skipped the version 1.51i [3] which is > the one currently packaged in Debian. I would prefer not have to > fudge anything. > > I managed to change the imagej package to also build the imagej > javadocs and have an extra libimagej-java-docs package for it. > However, this currently fails due to a bug on ImageJ which I believed > is fixed on later releases. Maybe this is the reason why ImageJA > skipped version 1.51i since they also release javadocs. > > --- > > Since I would be adding a libimagej-java-doc packages, maybe it would > make sense to have the pair libimagej-java? The lib package would > just package /use/share/java/ij.jar while the imagej package would > have the actual ImageJ program. > > Carnë > > [1] http://imagej.net/ImageJA > [2] https://github.com/carandraug/debian-imagej/commit/6ef7c9836d22b48 > [3] http://maven.imagej.net/content/groups/public/net/imagej/ij/ > > -- http://fam-tille.de
