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The Genome Modeling System installer
https://github.com/genome/gms/wiki
GNU Lesser General Public License v3.0
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'pdftk' not found #184

Closed gatoravi closed 9 years ago

gatoravi commented 9 years ago

clin-seq fails with this error,

   441 2015-03-30 20:14:17-0500 clia1: bash: pdftk: command not found
   442 2015-03-30 20:14:17-0500 clia1: Command module died or returned undef.
   443 2015-03-30 20:14:17-0500 clia1: ERROR RUNNING COMMAND.  Exit code 127 from: pdftk /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-             gmsuser-14730-6c4ea902bbf64f588e2de87c6b7b7232/2891323123-PicardGC_chart.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-gmsuser-          14730-6c4ea902bbf64f588e2de87c6b7b7232/2891323123-PicardMetrics.insert_size_histogram.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.         edu-gmsuser-14730-6c4ea902bbf64f588e2de87c6b7b7232/2891323123-PicardMetrics.quality_by_cycle.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.        wustl.edu-gmsuser-14730-6c4ea902bbf64f588e2de87c6b7b7232/2891323123-PicardMetrics.quality_distribution.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-        clia1.gsc.wustl.edu-gmsuser-14731-557ee05bbbec4d66878446eba208c3ab/2891323124-PicardGC_chart.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.        wustl.edu-gmsuser-14731-557ee05bbbec4d66878446eba208c3ab/2891323124-PicardMetrics.insert_size_histogram.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-       clia1.gsc.wustl.edu-gmsuser-14731-557ee05bbbec4d66878446eba208c3ab/2891323124-PicardMetrics.quality_by_cycle.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/         bam_qc-clia1.gsc.wustl.edu-gmsuser-14731-557ee05bbbec4d66878446eba208c3ab/2891323124-PicardMetrics.quality_distribution.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/                             build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-gmsuser-14660-ec2d0321912d45debc093ecc86cc6dce/2891323125-PicardGC_chart.pdf /opt/gms/MIW3W09/fs/MIW3W09/info/                  build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-gmsuser-14660-ec2d0321912d45debc093ecc86cc6dce/2891323125-PicardMetrics.insert_size_histogram.pdf /opt/gms/MIW3W09/fs/          MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-gmsuser-14660-ec2d0321912d45debc093ecc86cc6dce/2891323125-PicardMetrics.quality_by_cycle.pdf /opt/gms/             MIW3W09/fs/MIW3W09/info/build_merged_alignments/bam_qc/bam_qc-clia1.gsc.wustl.edu-gmsuser-14660-ec2d0321912d45debc093ecc86cc6dce/2891323125-PicardMetrics.quality_distribution.pdf        cat output /opt/gms/MIW3W09/fs/MIW3W09/info/model_data/18177dd5eca44514a47f367d9804e17a/buildd9155c0d0adc4e11a825a483a20f7196/TST1/input//wgs/summary_bam_qc/normal/                      24457aaebc1d44379a0d23823f49a2ff.pdf
gatoravi commented 9 years ago

pdftk was added to the list of the utils being installed here

gatoravi commented 9 years ago

This is fixed now, we need to test this on a fresh install before closing.

gatoravi commented 9 years ago

This seems to be working now.