igv_plotter syntax

[jungminchoilab]

Hello, I have been trying to run igv_plotter that was built from git.
The test run went through as shown below.

 [jc2545@login-0-0 igv_plotter]$ python setup.py test
 running test
 running egg_info 
 writing requirements to igv_plotter.egg-info/requires.txt
 writing igv_plotter.egg-info/PKG-INFO
 writing top-level names to igv_plotter.egg-info/top_level.txt
 writing dependency_links to igv_plotter.egg-info/dependency_links.txt
 reading manifest file 'igv_plotter.egg-info/SOURCES.txt'
 reading manifest template 'MANIFEST.in'
 writing manifest file 'igv_plotter.egg-info/SOURCES.txt'
 running build_ext
 test_execute_method (tests.test_igv_api.TestBasicUseCases) ... 0 commands to execute.
 Executing commands:
   new
   exit
 ok
 test_goto_locus_or_region (tests.test_igv_api.TestBasicUseCases) ... ok
 test_igv_command_line_robot_constructor (tests.test_igv_api.TestBasicUseCases) ... ok
 test_igv_robot_parent_class (tests.test_igv_api.TestBasicUseCases) ... Executing commands:
   new
   load file1.bam
   load file1.bam,file2.bam
   collapse
   squish
   expand
   viewaspairs
   genome hg18
   maxPanelHeight 30
   goto Y:1000
   goto 3:10-1000
   goto M:1000
   goto chr14:1000,chr3:12345
   goto X:1000,Y:12345
   region X 10 1000
   region chrMT 20 2000
   snapshot
   snapshot file1.png
   snapshot file2.png
   preference DEFAULT_FONT_SIZE 20
   exit
 ok
 test_load_method (tests.test_igv_api.TestBasicUseCases) ... Executing commands:
   load f.bam
   collapse f.bam
 Executing commands:
   load f.bam
   squish f.bam
 Executing commands:
   load f.bam
   expand f.bam
 Executing commands:
   load f.bam
   expand f.bam
   viewaspairs f.bam
 ok

 ----------------------------------------------------------------------
 Ran 5 tests in 0.005s

Then, I tried to follow the usage provided below.

[jc2545@compute-7-13 plotreads]$ igv_plotter -h
usage: igv_plotter [-h] [-o OUTPUT] [-L LOCUS_FILE] [-v] [--width WIDTH]
                   [--height HEIGHT] [--max-panel-height MAX_PANEL_HEIGHT]
                   [-c CONFIG_FILE] [-m MAX_MEMORY] [-g GENOME] [-p KEY=VALUE]
                   [--view-as-pairs] [--igv-jar-path IGV_JAR_PATH]
                   [--expand | --squish | --collapse]
                   files or loci [files or loci ...]

This script takes IGV snapshots. Args that start with '--' (eg. -o) can also be set in a config file (~/.igv_plotter or igv_plotter.yaml or specified via -c). The recognized syntax for setting (key, value) pairs is based on the INI and YAML formats (e.g. key=value or foo=TRUE). For full documentation of the differences from the standards please refer to the ConfigArgParse documentation. If an arg is specified in more than one place, then commandline values override config file values which override defaults.

optional arguments:
  -h, --help            show this help message and exit

core arguments:
  -o OUTPUT, --output OUTPUT
                        Output image file prefix (default: igv_)
  -L LOCUS_FILE, --locus-file LOCUS_FILE
                        Text file with one locus per line formatted like X:12345 or chr1:12345-54321. A snapshot will be taken at each locus. (default: None)
  files or loci         Files to load into IGV and/or loci at which to take snapshots (as an alternative to -L). Locus format can be X:12345 or chr1:12345-54321. Files and loci will be processed in the order they are specified, so if the command line order is 'file1.bed 1:12345 file2.bed', file1 will be loaded, then a snapshot will be taken, then file2 will be loaded. For a list of accepted IGV file formats, see https://www.broadinstitute.org/igv/RecommendedFileFormats
  -v, --verbose         Show log messages from igv_plotter and IGV. (default: False)
  --igv-jar-path IGV_JAR_PATH
                        Path to igv.jar (default: /ycga-ba/home/jc2545/.local/lib/python2.7/site-packages/igv_plotter-0.9.5-py2.7.egg/EGG-INFO/scripts/igv.jar)

additional options (YMMV - sometimes IGV ignores these):
  --width WIDTH         IGV window width. (default: 800)
  --height HEIGHT       IGV window height. (default: 600)
  --max-panel-height MAX_PANEL_HEIGHT
                        IGV max panel height. (default: 600)
  -c CONFIG_FILE, --config-file CONFIG_FILE
                        Config file path (default: None)
  -m MAX_MEMORY, --max-memory MAX_MEMORY
                        IGV max memory limit (eg. 2G) (default: 1024M)
  -g GENOME, --genome GENOME
                        Either the local path of a .genome file, or a genome id (eg. hg19) chosen from the right-most column of http://igv.broadinstitute.org/genomes/genomes.txt (default: hg19)
  -p KEY=VALUE, --preference KEY=VALUE
                        Changes one of the IGV settings (eg. -p DEFAULT_FONT_SIZE=10). For a full list of keys & example values that can be set, see: https://github.com/broadinstitute/IGV/blob/master/src/org/broad/igv/PreferenceManager.java#L928 (default: None)
  --view-as-pairs       In .bam tracks, view reads as pairs (default: False)
  --expand              Expand all tracks (default: None)
  --squish              Squish all tracks (default: None)
  --collapse            Collapse all tracks (default: None)

But it complains that file or directory cannot be found (e.g. I wanted to plot a locus 19:38994995 in VR14.bam).

[jc2545@compute-7-13 plotreads]$ igv_plotter -o RYR1 --igv-jar-path /ycga-ba/home/jc2545/programs/igv_plotter/lib/igv.jar -v -g /home/jc2545/ref_data/h_sapiens/1000genomes/2.5/b37/human_g1k_v37_decoy.fasta /ycga-ba/labs/lifton/jc2545/Zaidi/VR14/VR14.bam 19:38994995
INFO:root:Executing commands:
INFO:root:  genome /home/jc2545/ref_data/h_sapiens/1000genomes/2.5/b37/human_g1k_v37_decoy.fasta
INFO:root:  load /ycga-ba/labs/lifton/jc2545/Zaidi/VR14/VR14.bam
INFO:root:  maxPanelHeight 600
INFO:root:  goto 19:38994995
INFO:root:  snapshot RYR1s1__19_38994995.png
INFO:root:  exit
INFO:root:Hiding IGV window.
Traceback (most recent call last):
  File "/home/jc2545/.local/bin/igv_plotter", line 4, in <module>
    __import__('pkg_resources').run_script('igv-plotter==0.9.5', 'igv_plotter')
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 517, in run_script
  File "build/bdist.linux-x86_64/egg/pkg_resources.py", line 1436, in run_script
  File "/ycga-ba/home/jc2545/.local/lib/python2.7/site-packages/igv_plotter-0.9.5-py2.7.egg/EGG-INFO/scripts/igv_plotter", line 140, in <module>
    igv_robot.execute()
  File "/ycga-ba/home/jc2545/.local/lib/python2.7/site-packages/igv_plotter-0.9.5-py2.7.egg/igv_api.py", line 256, in execute
    self._execute_impl(self.__command_queue)
  File "/ycga-ba/home/jc2545/.local/lib/python2.7/site-packages/igv_plotter-0.9.5-py2.7.egg/igv_api.py", line 387, in _execute_impl
    fake_display.start()
  File "build/bdist.linux-x86_64/egg/xvfbwrapper.py", line 54, in start
  File "/home/jc2545/python/lib/python2.7/subprocess.py", line 710, in __init__
    errread, errwrite)
  File "/home/jc2545/python/lib/python2.7/subprocess.py", line 1327, in _execute_child
    raise child_exception
OSError: [Errno 2] No such file or directory

Can you please correct my command-line?
Thank you!