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Gaius-Augustus / GUSHR

Generating UTRs from SHort Reads
GNU General Public License v3.0
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GeMoMa 1.7.1 compatibiilty #3

Open nathanweeks opened 3 years ago

nathanweeks commented 3 years ago

GUSHR is currently incompatible with the latest GeMoMa release (version 1.7.1). This can be illustrated by minimally adapted GUSHR to accept the GeMoMa-1.7.1.jar file:

--- a/gushr.py
+++ b/gushr.py
@@ -153,3 +153,3 @@ else:
     this_script_path = os.path.dirname(os.path.realpath(sys.argv[0]))
-    jar = this_script_path + "/GeMoMa-1.6.2.jar"
+    jar = this_script_path + "/GeMoMa-1.7.1.jar"

And running the example as described in the README.md

 ./gushr.py -t example/augustus.gtf -b example/RNAseq.bam -g example/genome.fa -o utrs
...
Error in file ./gushr.py at line 281: Return code of subprocess was 1['/usr/bin/java', '-jar', '/scratch/user/repos/GUSHR/GeMoMa-1.7.1.jar', 'CLI', 'AnnotationFinalizer', 'u=YES', 'g=example/genome.fa', 'a=./gushr-BKQYSACALXGX/complete_gemoma_like.gff3', 'i=./gushr-BKQYSACALXGX/introns.gff', 'c=UNSTRANDED', 'coverage_unstranded=./gushr-BKQYSACALXGX/coverage.bedgraph', 'rename=NO', 'outdir=./gushr-BKQYSACALXGX/']

Invoking GeMoMa directly (so stdout/stderr aren't discarded by the gushr.py script):

$ java -jar GeMoMa-1.7.1.jar CLI AnnotationFinalizer u=YES g=example/genome.fa a=./gushr-BKQYSACALXGX/complete_gemoma_like.gff3 i=./gushr-BKQYSACALXGX/introns.gff c=UNSTRANDED coverage_unstranded=./gushr-BKQYSACALXGX/coverage.bedgraph rename=NO outdir=./gushr-BKQYSACALXGX/
...
Exception in thread "main" java.lang.NullPointerException
    at projects.gemoma.AnnotationFinalizer.read(AnnotationFinalizer.java:418)
    at projects.gemoma.AnnotationFinalizer.run(AnnotationFinalizer.java:516)
    at projects.gemoma.AnnotationFinalizer.run(AnnotationFinalizer.java:468)
    at projects.gemoma.GeMoMaModule.run(GeMoMaModule.java:92)
    at de.jstacs.tools.ui.cli.CLI.run(CLI.java:426)
    at projects.gemoma.GeMoMa.main(GeMoMa.java:378)