Struggling to Install

[danphillips28]

Hello! Thanks for making this interesting tool. I am trying to install ciri2 on a cluster but I am struggling.

I am following the CIRI cookbook https://ciri-cookbook.readthedocs.io/_/downloads/en/latest/pdf/.

I have found and (seemingly) installed CIRI_v2.0.6.zip, however this is not sufficient to run the full pipeline.

To use CIRI-full.jar, the cookbook directs me to download and unzip CIRI-full.zip. I have not been able to find CIRI-full.zip, only CIRI_Full_v2.1.1.jar (from https://sourceforge.net/projects/ciri/files/CIRI-full/CIRI_Full_v2.1.1.jar/download). I tried to unzip this instead, as follows;

#!/bin/bash
module load Perl/5.34.0-GCCcore-11.2.0
module load Python/3.9.6-GCCcore-11.2.0
module load BWA/0.7.17-GCCcore-11.2.0
unzip CIRI_Full_v2.1.1.jar
module purge

This produced a bunch of files and directories;
replace .project? [y]es, [n]o, [A]ll, [N]one, [r]ename:
inflating: reversc.java
inflating: Exon_cov2.java
inflating: Exon_gtf.java
inflating: sam5.java
inflating: index_head_finder2.java
inflating: RO2.java
inflating: index_head_finder_more.java
inflating: Merge3.java
inflating: CIRI_Full2.java
inflating: Seq.java
inflating: Exon_length.java
inflating: RO1_single.java
inflating: CIRI_Full2$1.class
inflating: CIRI_Full2$2.class
inflating: CIRI_Full2$3.class
inflating: CIRI_Full2$4.class
inflating: CIRI_Full2.class
inflating: Exon_cov2.class
inflating: Exon_gtf.class
inflating: Exon_length.class
inflating: Merge3.class
inflating: RO1_single.class
inflating: RO2.class
inflating: Seq.class
inflating: index_head_finder2.class
inflating: index_head_finder_more.class
inflating: reversc.class
inflating: sam5.class

However, trying to run CIRI_FULL2.java using the cookbook code produces the following error:
$ java -jar CIRI_Full_v2.1.1.jar
Error occurred during initialization of VM
Could not allocate metaspace: 1073741824 bytes

Overall, I am unclear on how to install your tool and the cookbook isn't helping. Please provide some guidance.
Thanks,
Dan

[Kevinzjy]

Hi @danphillips28, this is not a CIRI-full issue.

The CIRI-full.jar is executable through the java -jar CIRI-full.jar command directly, there's no need to install it. And the Could not allocate metaspace: 1073741824 bytes error means you do not have enough memory (1GB) for running JVM.

I guess that you're running CIRI-full on a HPC and forget to set the memory usage parameters.