sandy

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remove calls to undefined App::Sandy::Types->import

1

App::Sandy::Types does not export anything, and has no import method. The calls to its import method were ignored by perl. Future versions of perl are intending to throw errors for...

haarg

Dear developer ``` docker run --rm -v variants_PASS.vcf:/variants_PASS.vcf -v sandy_db:/sandy/db galantelab/sandy variation add --verbose -a entry variants_PASS.vcf :: Inserting entry from variants_PASS.vcf ... :: Checking if there is already a...

a00101

Dear developer First of all, thank you for nice tool. Is there a way to have WGS and RNA-sequencing data produced by one person from sandy?

a00101

On systems where the default make is not GNU make, e.g. on FreeBSD systems, the build step fails. On older FreeBSD systems: ``` Output from '/usr/bin/make': make: "/home/cpansand/.cpan/build/2023092409/App-Sandy-0.25-vurlG2/Makefile" line 1560:...

eserte

Cpantesters at the moment has three fail reports that look very similar: http://www.cpantesters.org/cpan/report/ac26ae6a-62d8-11eb-a7b1-5e721f24ea8f http://www.cpantesters.org/cpan/report/2e789072-a7c5-11ec-9d95-7f323e235ef0 http://www.cpantesters.org/cpan/report/1c563258-a835-11ec-bf1f-3d4ddc81be55 I produced the last one by simply letting the test run repeatedly in a loop...

andk

Congrats on Dr. Galante's team for the excellent work that went in making this tool! I am using sandy in a project that's about to be submitted and wanted to...

rdalbanus

Hi, After generating reads with Sandy and using a Nanopore quality-profile, I noticed that some reads have a length of one base. There should be a way to allow for...

OSantt

Circular Genome

2

Dear Developers, I have a doubt, does this program generate reads by assuming a circular genome? If not, is there a chance to make it possible? Greetings.

EnzoAndree

Undeclared dependency File::ShareDir::Install

1

On one of my smokers: ``` Output from '/usr/local/bin/perl Makefile.PL': Can't locate File/ShareDir/Install.pm in @INC (you may need to install the File::ShareDir::Install module) (@INC contains: /var/tmp/cpansmoker-1023/2019031020/CPAN-Reporter-lib-aob4 /usr/local/lib/perl5/site_perl/mach/5.28 /usr/local/lib/perl5/site_perl /usr/local/lib/perl5/5.28/mach /usr/local/lib/perl5/5.28...

eserte

The test suite of App-Sandy-0.25 fails with newer perl versions (>=5.40): ``` "/opt/perl-5.40.0/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- RNG.bs blib/arch/auto/App/Sandy/RNG/RNG.bs 644 PERL_DL_NONLAZY=1 "/opt/perl-5.40.0/bin/perl" "-MExtUtils::Command::MM" "-MTest::Harness" "-e" "undef *Test::Harness::Switches; test_harness(0, 'blib/lib', 'blib/arch')"...

eserte