Mercurial > repos > artbio > repenrich
changeset 14:bf866bedd4b4 draft
planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/main/tools/repenrich commit 205141a3f695f202d5c3e01e6ab3b2b869fe62b5
| author | artbio |
|---|---|
| date | Sat, 20 Apr 2024 12:13:52 +0000 |
| parents | 530626b0757c |
| children | 2e3d976e7d5d |
| files | RepEnrich.py RepEnrich_setup.py macros.xml |
| diffstat | 3 files changed, 1 insertions(+), 25 deletions(-) [+] |
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--- a/RepEnrich.py Tue Apr 02 21:16:37 2024 +0000 +++ b/RepEnrich.py Sat Apr 20 12:13:52 2024 +0000 @@ -1,6 +1,5 @@ import argparse import csv -import os import shlex import subprocess import sys @@ -46,18 +45,6 @@ else: paired_end = False -# check that the programs we need are available -try: - subprocess.call(shlex.split("coverageBed -h"), - stdout=open(os.devnull, 'wb'), - stderr=open(os.devnull, 'wb')) - subprocess.call(shlex.split("bowtie --version"), - stdout=open(os.devnull, 'wb'), - stderr=open(os.devnull, 'wb')) -except OSError: - print("Error: Bowtie or bedtools not loaded") - raise - def starts_with_numerical(list): try:
--- a/RepEnrich_setup.py Tue Apr 02 21:16:37 2024 +0000 +++ b/RepEnrich_setup.py Sat Apr 20 12:13:52 2024 +0000 @@ -1,7 +1,6 @@ #!/usr/bin/env python import argparse import csv -import os import shlex import subprocess import sys @@ -48,15 +47,6 @@ genomefasta = args.genomefasta cpus = args.cpus -# check that the programs we need are available -try: - subprocess.call(shlex.split("bowtie --version"), - stdout=open(os.devnull, 'wb'), - stderr=open(os.devnull, 'wb')) -except OSError: - print("Error: Bowtie not available in the path") - raise - def starts_with_numerical(list): try: @@ -115,7 +105,6 @@ block = 3 for i in range(0, len(rep_coords[repname]) - block + 1, block): batch = rep_coords[repname][i:i+block] - print(batch) chromosome = batch[0] start = max(int(batch[1]) - flankingl, 0) end = min(int(batch[2]) + flankingl,
--- a/macros.xml Tue Apr 02 21:16:37 2024 +0000 +++ b/macros.xml Sat Apr 20 12:13:52 2024 +0000 @@ -1,6 +1,6 @@ <macros> <token name="@TOOL_VERSION@">2.31.1</token> - <token name="@VERSION_SUFFIX@">0</token> + <token name="@VERSION_SUFFIX@">1</token> <token name="@PROFILE@">23.0</token> <xml name="repenrich_requirements">