Curl issue in Makefile when downloading htsjdk

[xchrom]

Hi Pierre,

While using jvarkit for the first time, I ran into an issue when compiling sam2tsv and wanted to let others know the solution in case they encountered a similar issue.

I kept getting an error with curl and ca certificates when trying to compile sam2tsv

$ make sam2tsv

mkdir -p /home4/user/software/jvarkit/ rm -rf /home4/user/software/jvarkit/2.0.1.zip /home4/user/software/jvarkit/htsjdk-2.0.1/ echo "Downloading HTSJDK 2.0.1 with curl" Downloading HTSJDK 2.0.1 with curl curl -o /home4/user/software/jvarkit/2.0.1.zip -L "https://github.com/samtools/htsjdk/archive/2.0.1.zip" % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0curl: (77) error setting certificate verify locations: CAfile: /etc/pki/tls/certs/ca-bundle.crt CApath: none make: *\ [home4/user/software/jvarkit/htsjdk-2.0.1/build.xml] Error 77

I went and looked Makefile and found that by adding the -k option (allows insecure transfers), everything worked great. Every other time curl was in used Makefile it had the -k option.

line 589: curl -k ${curl.proxy} -o $(dir ${htsjdk.home})${htsjdk.version}.zip -L "https://github.com/samtools/htsjdk/archive/${htsjdk.version}.zip"

[lindenb]

thanks ! I'll had the -k for downloading htsjdk.

[lindenb]

done: https://github.com/lindenb/jvarkit/commit/d0200d5e4e653bfdeadbb40efa588d4fd31706fe