span: span_wrapper.py annotate

annotate span_wrapper.py @ 6:70500fd87b60 draft

Advanced options: threads and memory configuration

author	jetbrains
date	Wed, 21 Nov 2018 10:31:58 -0500
parents	4130e95bd6c8
children

rev	line source
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	1 #!/usr/bin/env python
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	2
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	3 import os
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	4 import shutil
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	5 import subprocess
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	6 import sys
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	7
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	8 argv = sys.argv[1:]
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	9 print 'Arguments {0}'.format(argv)
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	10
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	11 SPAN_JAR = os.environ.get("SPAN_JAR")
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	12 print 'Using SPAN Peak Analyzer distributive file {0}'.format(SPAN_JAR)
1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	13
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	14 MEMORY = argv[0]
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	15 THREADS = argv[1]
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	16 ACTION = argv[2]
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	17 argv = argv[3:]
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	18
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	19 working_dir = os.path.abspath('.')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	20 print 'WORKING DIRECTORY: {}'.format(working_dir)
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	21
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	22
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	23 def link(name, f):
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	24 """ SPAN uses file extension to detect input type, so original names are necessary, instead of Galaxy .dat files"""
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	25 result = os.path.join(working_dir, name)
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	26 if not os.path.exists(result):
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	27 os.symlink(f, result)
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	28 return result
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	29
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	30
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	31 if ACTION == 'model_with_control':
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	32 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	33 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	34 control, control_file,
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	35 bin) = argv
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	36 cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	37 '--chrom.sizes {} --treatment {} --control {} --bin {}'.format(
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	38 MEMORY, SPAN_JAR, THREADS,
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	39 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	40 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	41 link(control, control_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	42 bin)
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	43
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	44 elif ACTION == 'model_without_control':
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	45 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	46 treatment, treatment_file,
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	47 bin) = argv
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	48 cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	49 '--chrom.sizes {} --treatment {} --bin {}'.format(
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	50 MEMORY, SPAN_JAR, THREADS,
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	51 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	52 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	53 bin)
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	54
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	55 elif ACTION == "peaks_with_control":
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	56 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	57 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	58 control, control_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	59 bin,
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	60 fdr, gap) = argv
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	61 cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	62 '--chrom.sizes {} --treatment {} --control {} --bin {} --fdr {} --gap {} --peaks {}'.format(
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	63 MEMORY, SPAN_JAR, THREADS,
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	64 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	65 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	66 link(control, control_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	67 bin, fdr, gap,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	68 os.path.join(working_dir, 'result.peak'))
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	69
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	70 elif ACTION == 'peaks_without_control':
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	71 (chrom_sizes, chrom_sizes_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	72 treatment, treatment_file,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	73 bin,
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	74 fdr, gap) = argv
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	75 cmd = 'java -Xmx{}m -jar {} analyze --threads {} ' \
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	76 '--chrom.sizes {} --treatment {} -bin {} --fdr {} --gap {} --peaks {}'.format(
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	77 MEMORY, SPAN_JAR, THREADS,
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	78 link(chrom_sizes, chrom_sizes_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	79 link(treatment, treatment_file),
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	80 bin, fdr, gap,
4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	81 os.path.join(working_dir, 'result.peak'))
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	82 (chrom_sizes, chrom_sizes_file,
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	83 treatment, treatment_file,
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	84 bin,
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	85 fdr, gap) = argv
70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	86
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	87 else:
6 70500fd87b60 Advanced options: threads and memory configuration jetbrains parents: 3 diff changeset	88 raise Exception("Unknown action command {}".format(ACTION))
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	89
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	90 print 'Launching SPAN: {}'.format(cmd)
0 1f0c4f0a9c3b Initial version of SPAN for ToolShed jetbrains parents: diff changeset	91 subprocess.check_call(cmd, cwd=None, shell=True)
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	92
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	93 # Move model to the the working dir with given name
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	94 fit_dir = os.path.join(working_dir, 'fit')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	95 model_original = os.path.join(fit_dir, os.listdir(fit_dir)[0])
3 4130e95bd6c8 Batch processing mode supported jetbrains parents: 2 diff changeset	96 shutil.move(model_original, os.path.join(working_dir, 'model.span'))
2 5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	97
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	98 # Move log file
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	99 logs_dir = os.path.join(working_dir, 'logs')
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	100 log_original = os.path.join(logs_dir, os.listdir(logs_dir)[0])
5b99943c4627 Span version https://github.com/JetBrains-Research/galaxy-applications/commit/cbbba255d66a4775cc35caf5cb85665396fdcd2a jetbrains parents: 0 diff changeset	101 shutil.move(log_original, os.path.join(working_dir, "span.log"))

Mercurial > repos > jetbrains > span

annotate span_wrapper.py @ 6:70500fd87b60 draft