On Wed, 6 Jun 2018 at 08:06 Andreas Tille <[email protected]> wrote: > Hi Liubov, > > On Wed, Jun 06, 2018 at 12:16:38AM +0200, Liubov Chuprikova wrote: > > > > I have just added tests. Unfortunately, I could not test gmer_counter and > > gmer_caller, as they require a lot of memory to allocate (it is > hardcoded). > > I think it is OK to test only part of the tools. May be you can inform > upstream by opening an issue that the hard coded memory could create > trouble in practical applications. >
Thanks for the idea! I have checked and they are already appeared to have one issue opened [1]. Except it is stated to be about compressed input files, not about memory, I got the same error and the problem was definitely with running out of memory. I'll write a bit later to this issue, too. > Please, take a look at the package! I think that it could be uploaded if I > > have not missed something critical. > > Not really critical but please add some information about the test data > sets in README.source - preferably some "wget ..." or so. > I put info about test data files in d/copyright. Should I transfer it to README.source instead? PS: Once you have added this do you know with which package you want to > continue or should I make some suggestions? > I thought about these packages: ncbi-entrez-direct, sra-sdk, rsem, soapdenovo, soapdenovo2, kmer, treeview, fastdnaml. Not sure about artemis. All are familiar to me to some extent. I'll be happy to have any suggestions or recommendations from you! :-) With regards, Liubov [1] https://github.com/bioinfo-ut/GenomeTester4/issues/4
