Error: Invalid or corrupt jarfile

[mherold1]

Hello,

thanks for providing this tool, after reading the preprint I wanted to try it out.
After the installation and adapting the config.properties file I tried to run it on the example dataset and got:

$ java -jar PoolHapX.jar script Example_Data/config.properties
Error: Invalid or corrupt jarfile PoolHapX.jar

Do you have an idea what could be going wrong here?

$ java -version
openjdk version "1.8.0_265"
OpenJDK Runtime Environment (Zulu 8.48.0.53-CA-linux64) (build 1.8.0_265-b11)
OpenJDK 64-Bit Server VM (Zulu 8.48.0.53-CA-linux64) (build 25.265-b11, mixed mode)

Also I noticed in the comments in config.properties file:

#If Sequencing_Technology is paired-end reads, users may leave the parameter "bwa" blank.
bwa = bwa
#If Sequencing_Technology is 10x_linked-reads, users may leave the parameter "longranger" blank.
longranger = 
#/PATH/TO/longranger_ref_folde is generated by the "mkref" function of longranger. If Sequencing_Technology is 10x_linked-reads, users may leave the parameter "Longranger_Ref_Folder" blank.

Shouldn't this be the other way around, I thought longranger is only used if the input is 10x linked-reads?

[gavinmdouglas]

Regarding your first question I ran into the same problem and I believe it is because the jarfile is really large and so you need git lfs installed. In my case I also needed to run these commands after cloning the repo (even though git lfs was installed beforehand):

git lfs install
git lfs pull

The jarfile (and possibly other large files) were downloaded properly after running those commands.