invalid literal for int() with base 10 error

[kaanokay]

Hi,

First of all, thank you for this script-based IGV visualization.

When I run your demo dataset and also mine, I obtained error that I attached it as screenshot below:

Can I solve this issue?

Thanks for your interest.

Best wishes.

[stevekm]

You might try commenting out these two lines;

IGV-snapshot-automator/make_IGV_snapshots.py

Lines 223 to 224 in d2c01a5

	x_serv_port = get_open_X_server()
	print('\nOpen Xvfb port found on:\n{}\n'.format(x_serv_port))

I had previously been using this method to obtain an open xvfb server number;

IGV-snapshot-automator/make_IGV_snapshots.py

Lines 120 to 135 in d2c01a5

	def get_open_X_server():
	'''
	Search for an open Xvfb port to render into
	'''
	x_serv_command= '''
	for serv_num in $(seq 1 1000); do
	if ! (xdpyinfo -display :${serv_num})&>/dev/null; then
	echo "$serv_num" && break
	fi
	done
	'''
	import subprocess as sp
	# run the command, capture the output
	process = sp.Popen(x_serv_command,stdout=sp.PIPE, shell=True)
	x_serv_port = int(process.communicate()[0].strip())
	return(x_serv_port)

However I later found that many systems include xvfb-run --auto-servernum method which I switched over to using here;

IGV-snapshot-automator/make_IGV_snapshots.py

Line 227 in d2c01a5

igv_command = "xvfb-run --auto-servernum --server-num=1 java -Xmx{}m -jar {} -b {}".format(memMB, igv_jar, igv_script)

however the original call to xdpyinfo is still present and it appears that the version on your system is giving a different response than expected.

If commenting out that works for you I can make a fix in the script for it as well. Thanks.

[stevekm]

this whole process is a little tricky since it seems like different systems have slightly different versions of xdpyinfo and xvfb-run which can cause problems like this.

[stevekm]

marking this as a bug that I should probably fix; just get rid of the old command that is not needed anymore