Update bioconda?
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Hi! Thank you for providing this tool :) . I tried installing it with conda as described in the README, but it seems like the newest version is not available https://anaconda.org/bioconda/tiddit . Would it be possible to update it there?
Hello!
And thanks for running tiddit!
Sorry for the inconvenience, I have been working on a new major version of tiddit, reimplemented in python and with local assembly:
https://github.com/J35P312/TIDDIT/tree/develop
Hence, I have not given the tiddit conda the attention it deserves!
I will be away rest of the week, but I will check if I can quickly update tiddit on conda; otherwise, I will do so once the new version is released, that would be before the end of february.
I will keep you posted!
Best regards Jesper
Sounds great looking forward to both the new release and the conda update :)
great news!
Hi! any update on the ETA of the release? :)
Hello!
And sorry for not coming back to you!
The latest tiddit release is pushed and merged into bioconda:
bioconda/bioconda-recipes#32756
However it is still not available:
https://anaconda.org/bioconda/tiddit/files
I will look into this later; do you have experience with bioconda, maybe you have a suggestion how to fix this?
The new major update is more or less done! I have been running it on about 100 clinical cases with known pathogenic SV, now I plan to check and see that those SV were found properly. If everything looks good I will update!
Have a nice day!
Hi! Oh awesome 🥳 I did not see it. Unfortuantely, none. I was just going to ask there. I mean all the test passed 🤔
Hi @J35P312 !
Looks like there are still issues publishing the package 🙈 https://anaconda.org/bioconda/tiddit
I guess it is still maybe blacklisted?! I tried white listing it bioconda/bioconda-recipes#33833 , and immediately nothing worked anymore, but I also have to say that I have absolutely no idea what I am doing when it comes to conda recipe building.
ah ok, I see now the follow up PR couldn't be merged due to some dependency conflicts bioconda/bioconda-recipes#33906 Leaving the link here in case someone else stumbles over it
Hello!
Sorry for the delay! I was away on a conference last week!
Though luck! But thanks for trying =P.
I'm now done with the V 3.0.0, where I have replaced old bamtools api with pysam; hence there should be no issues with the compiler.
I will make a new conda recipe for 3.0.0, hopefully I will be done by the end of next week!
Meanwhile, you are free to try TIDDIT 3.0.0 here:
https://github.com/J35P312/TIDDIT
Thanks for your patience!
//JEsper
uh sweet. Thanks a lot :) I will see if I can try it out this week
Hey! congrats, I saw the release https://github.com/J35P312/TIDDIT/releases/tag/TIDDIT-3.0.0 . Unfortunately the conda package could still not be build 🙈 bioconda/bioconda-recipes#34759 Do you think it will be fixable?
Hello!
Thanks =P.
Woopsiedaisy! There seems to be some issue with the linting. The build logs are removed, but I tried linting locally:
The following problems have been found:
ERROR: recipes/tiddit/meta.yaml:0: cython_must_be_in_host: Cython should be in the host section
Errors were found
however, cython is already in the host section (line 22) ... I have no idea how to fix that! For now, I will probably skip conda and go back to using docker.
Sorry!
https://anaconda.org/bioconda/tiddit Tiddit 3.0 is there now :)
That is great news!
Well done, and thanks a lot, I will give it a try =P.