Mercurial > repos > peterjc > mira4_assembler
changeset 35:259891fce7fd draft
planemo upload for repository https://github.com/peterjc/galaxy_mira/tree/master/tools/mira4_0 commit e4c56df75150c82d3e9c4ac487c4209108e52412
| author | peterjc |
|---|---|
| date | Wed, 09 Aug 2017 13:32:11 -0400 |
| parents | 0785a6537f3e |
| children | 46d73b942b43 |
| files | tools/mira4_0/README.rst tools/mira4_0/mira4.py tools/mira4_0/mira4_bait.py tools/mira4_0/mira4_bait.xml tools/mira4_0/mira4_convert.py tools/mira4_0/mira4_de_novo.xml tools/mira4_0/mira4_make_bam.py tools/mira4_0/mira4_mapping.xml tools/mira4_0/repository_dependencies.xml |
| diffstat | 9 files changed, 42 insertions(+), 34 deletions(-) [+] |
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--- a/tools/mira4_0/README.rst Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/README.rst Wed Aug 09 13:32:11 2017 -0400 @@ -111,6 +111,8 @@ v0.0.10 - Python 3 compatible syntax (internal change only). - Use ``<command detect_errors="aggressive">`` (internal change only). - Single quote command line arguments (internal change only). +v0.0.11 - For compatibility with MIRA installed from the BioConda package, + if ``MIRA4$`` is not set, assume binaries are on the ``$PATH``. ======= ======================================================================
--- a/tools/mira4_0/mira4.py Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4.py Wed Aug 09 13:32:11 2017 -0400 @@ -16,7 +16,7 @@ # Do we need any PYTHONPATH magic? from mira4_make_bam import make_bam -WRAPPER_VER = "0.0.10" # Keep in sync with the XML file +WRAPPER_VER = "0.0.11" # Keep in sync with the XML file def get_version(mira_binary): @@ -69,18 +69,21 @@ out_fasta = options.fasta out_log = options.log -try: +if "MIRA4" in os.environ: mira_path = os.environ["MIRA4"] -except KeyError: - sys.exit("Environment variable $MIRA4 not set") -mira_binary = os.path.join(mira_path, "mira") -if not os.path.isfile(mira_binary): - sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" - % (mira_binary, ", ".join(os.listdir(mira_path)))) -mira_convert = os.path.join(mira_path, "miraconvert") -if not os.path.isfile(mira_convert): - sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" - % (mira_convert, ", ".join(os.listdir(mira_path)))) + mira_binary = os.path.join(mira_path, "mira") + if not os.path.isfile(mira_binary): + sys.exit("Missing mira under $MIRA4, %r\nFolder contained: %s" + % (mira_binary, ", ".join(os.listdir(mira_path)))) + mira_convert = os.path.join(mira_path, "miraconvert") + if not os.path.isfile(mira_convert): + sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" + % (mira_convert, ", ".join(os.listdir(mira_path)))) +else: + sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") + mira_path = None + mira_binary = "mira" + mira_convert = "miraconvert" mira_ver = get_version(mira_binary) if not mira_ver.strip().startswith("4.0"):
--- a/tools/mira4_0/mira4_bait.py Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_bait.py Wed Aug 09 13:32:11 2017 -0400 @@ -10,7 +10,7 @@ import sys import time -WRAPPER_VER = "0.0.10" # Keep in sync with the XML file +WRAPPER_VER = "0.0.11" # Keep in sync with the XML file def get_version(mira_binary): @@ -37,14 +37,17 @@ return ver.split("\n", 1)[0] -try: +if "MIRA4" in os.environ: mira_path = os.environ["MIRA4"] -except KeyError: - sys.exit("Environment variable $MIRA4 not set") -mira_binary = os.path.join(mira_path, "mirabait") -if not os.path.isfile(mira_binary): - sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s" - % (mira_binary, ", ".join(os.listdir(mira_path)))) + mira_binary = os.path.join(mira_path, "mirabait") + if not os.path.isfile(mira_binary): + sys.exit("Missing mirabait under $MIRA4, %r\nFolder contained: %s" + % (mira_binary, ", ".join(os.listdir(mira_path)))) +else: + sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") + mira_path = None + mira_binary = "mirabait" + mira_ver = get_version(mira_binary) if not mira_ver.strip().startswith("4.0"): sys.exit("This wrapper is for MIRA V4.0, not:\n%s" % mira_ver)
--- a/tools/mira4_0/mira4_bait.xml Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_bait.xml Wed Aug 09 13:32:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.10"> +<tool id="mira_4_0_bait" name="MIRA v4.0 mirabait" version="0.0.11"> <description>Filter reads using kmer matches</description> <requirements> <requirement type="package" version="4.0.2">MIRA</requirement>
--- a/tools/mira4_0/mira4_convert.py Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_convert.py Wed Aug 09 13:32:11 2017 -0400 @@ -22,7 +22,7 @@ # Do we need any PYTHONPATH magic? from mira4_make_bam import depad -WRAPPER_VER = "0.0.10" # Keep in sync with the XML file +WRAPPER_VER = "0.0.11" # Keep in sync with the XML file def run(cmd): @@ -110,14 +110,16 @@ out_ace = options.ace out_cstats = options.cstats -try: +if "MIRA4" in os.environ: mira_path = os.environ["MIRA4"] -except KeyError: - sys.exit("Environment variable $MIRA4 not set") -mira_convert = os.path.join(mira_path, "miraconvert") -if not os.path.isfile(mira_convert): - sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" - % (mira_convert, ", ".join(os.listdir(mira_path)))) + mira_convert = os.path.join(mira_path, "miraconvert") + if not os.path.isfile(mira_convert): + sys.exit("Missing miraconvert under $MIRA4, %r\nFolder contained: %s" + % (mira_convert, ", ".join(os.listdir(mira_path)))) +else: + sys.stderr.write("DEBUG: Since $MIRA4 is not set, assuming mira binaries are on $PATH.\n") + mira_path = None + mira_convert = "miraconvert" mira_convert_ver = get_version(mira_convert) if not mira_convert_ver.strip().startswith("4.0"):
--- a/tools/mira4_0/mira4_de_novo.xml Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_de_novo.xml Wed Aug 09 13:32:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.10"> +<tool id="mira_4_0_de_novo" name="MIRA v4.0 de novo assember" version="0.0.11"> <description>Takes Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> <requirements> <requirement type="package" version="4.0.2">MIRA</requirement>
--- a/tools/mira4_0/mira4_make_bam.py Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_make_bam.py Wed Aug 09 13:32:11 2017 -0400 @@ -56,8 +56,6 @@ def make_bam(mira_convert, maf_file, fasta_file, bam_file, log_handle): - if not os.path.isfile(mira_convert): - return "Missing binary %r" % mira_convert if not os.path.isfile(maf_file): return "Missing input MIRA file: %r" % maf_file if not os.path.isfile(fasta_file):
--- a/tools/mira4_0/mira4_mapping.xml Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/mira4_mapping.xml Wed Aug 09 13:32:11 2017 -0400 @@ -1,4 +1,4 @@ -<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.10"> +<tool id="mira_4_0_mapping" name="MIRA v4.0 mapping" version="0.0.11"> <description>Maps Sanger, Roche 454, Solexa/Illumina, Ion Torrent and PacBio reads</description> <requirements> <requirement type="package" version="4.0.2">MIRA</requirement>
--- a/tools/mira4_0/repository_dependencies.xml Wed Jun 07 12:33:39 2017 -0400 +++ b/tools/mira4_0/repository_dependencies.xml Wed Aug 09 13:32:11 2017 -0400 @@ -1,4 +1,4 @@ <?xml version="1.0"?> <repositories description="This requires the MIRA datatype definitions (e.g. the MIRA Assembly Format)."> - <repository changeset_revision="3fc6ff47a3b1" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> + <repository changeset_revision="f4d34bd3c633" name="mira_datatypes" owner="peterjc" toolshed="https://testtoolshed.g2.bx.psu.edu" /> </repositories>