# HG changeset patch
# User peterjc
# Date 1438788485 14400
# Node ID 63ebe9726219d39a4a2caa808c47b2ff5727ab2b
# Parent e59904c855ae3a1e508a406df55035817f2eec49
v0.0.11 move dependency to package_mira_3_4_1_1 etc
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/README.rst
--- a/tools/mira3/README.rst Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/README.rst Wed Aug 05 11:28:05 2015 -0400
@@ -30,10 +30,15 @@
* ``mira.xml`` (the Galaxy tool definition)
The suggested location is a new ``tools/mira3`` folder. You will also need to
-modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool, and also do
-this to ``tools_conf.xml.sample`` in order to run any tests::
+modify the ``tools_conf.xml`` file to tell Galaxy to offer the tool by adding
+the line::
+
+
-
+If you wish to run the unit tests, also move/copy the ``test-data/`` files
+under Galaxy's ``test-data/`` folder. Then::
+
+ $ ./run_tests -id mira_assembler
You will also need to install MIRA, we used version 3.4.1.1. See:
@@ -77,6 +82,9 @@
- Correct path issue in automated dependency installation.
v0.0.10 - Added a functional test.
- Updated URL for automated installation of MIRA v3.4.1.1
+v0.0.11 - Tool definition now embeds citation information.
+ - Planemo for Tool Shed upload (``.shed.yml``, internal change only).
+ - MIRA 3.4.1.1 dependency now declared via dedicated Tool Shed package.
======= ======================================================================
@@ -89,21 +97,30 @@
Development has now moved to a dedicated GitHub repository:
https://github.com/peterjc/pico_galaxy/tree/master/tools/mira_3_4
-For making the "Galaxy Tool Shed" http://toolshed.g2.bx.psu.edu/ tarball use
-the following command from the Galaxy root folder::
+For pushing a release to the test or main "Galaxy Tool Shed", use the following
+Planemo commands (which requires you have set your Tool Shed access details in
+``~/.planemo.yml`` and that you have access rights on the Tool Shed)::
- $ tar -czf mira3_wrapper.tar.gz tools/mira3/README.rst tools/mira3/mira.xml tools/mira3/mira.py tools/mira3/tool_dependencies.xml test-data/tvc_mini.fastq test-data/tvc_contigs.fasta test-data/empty_file.dat
+ $ planemo shed_update --shed_target testtoolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+ ...
-Check this worked::
+or::
+
+ $ planemo shed_update --shed_target toolshed --check_diff ~/repositories/pico_galaxy/tools/mira3/
+ ...
- $ tar -tzf mira3_wrapper.tar.gz
+To just build and check the tar ball, use::
+
+ $ planemo shed_upload --tar_only ~/repositories/pico_galaxy/tools/mira3/
+ ...
+ $ tar -tzf shed_upload.tar.gz
+ test-data/empty_file.dat
+ test-data/tvc_contigs.fasta
+ test-data/tvc_mini.fastq
tools/mira3/README.rst
- tools/mira3/mira.xml
tools/mira3/mira.py
+ tools/mira3/mira.xml
tools/mira3/tool_dependencies.xml
- test-data/tvc_mini.fastq
- test-data/tvc_contigs.fasta
- test-data/empty_file.dat
Licence (MIT)
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/mira.py
--- a/tools/mira3/mira.py Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/mira.py Wed Aug 05 11:28:05 2015 -0400
@@ -9,7 +9,7 @@
WRAPPER_VER = "0.0.5" #Keep in sync with the XML file
-def stop_err(msg, err=1):
+def sys_exit(msg, err=1):
sys.stderr.write(msg+"\n")
sys.exit(err)
@@ -33,7 +33,7 @@
mira_ver = get_version()
if "V3.4." not in mira_ver:
- stop_err("This wrapper is for MIRA V3.4, not %s" % mira_ver)
+ sys_exit("This wrapper is for MIRA V3.4, not %s" % mira_ver)
if "-v" in sys.argv:
print "MIRA wrapper version %s," % WRAPPER_VER
print mira_ver
@@ -44,9 +44,9 @@
n3 = (temp, name, name, name)
f = "%s/%s_assembly/%s_d_results" % (temp, name, name)
if not os.path.isdir(f):
- stop_err("Missing output folder")
+ sys_exit("Missing output folder")
if not os.listdir(f):
- stop_err("Empty output folder")
+ sys_exit("Empty output folder")
missing = []
for old, new in [("%s/%s_out.unpadded.fasta" % (f, name), out_fasta),
("%s/%s_out.unpadded.fasta.qual" % (f, name), out_qual),
@@ -58,7 +58,7 @@
else:
shutil.move(old, new)
if missing:
- stop_err("Missing output files: %s" % ", ".join(missing))
+ sys_exit("Missing output files: %s" % ", ".join(missing))
def clean_up(temp, name):
folder = "%s/%s_assembly" % (temp, name)
@@ -112,7 +112,7 @@
handle.write(cmd + "\n")
handle.close()
clean_up(temp, name)
- stop_err("Return error code %i from command:\n%s" % (return_code, cmd),
+ sys_exit("Return error code %i from command:\n%s" % (return_code, cmd),
return_code)
handle.close()
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/mira.xml
--- a/tools/mira3/mira.xml Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/mira.xml Wed Aug 05 11:28:05 2015 -0400
@@ -1,4 +1,4 @@
-
+
Takes Sanger, Roche, Illumina, and Ion Torrent data
mira
@@ -189,4 +189,16 @@
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
+
+ 10.7717/peerj.167
+ @ARTICLE{Chevreux1999-mira3,
+ author = {B. Chevreux and T. Wetter and S. Suhai},
+ year = {1999},
+ title = {Genome Sequence Assembly Using Trace Signals and Additional Sequence Information},
+ journal = {Computer Science and Biology: Proceedings of the German Conference on Bioinformatics (GCB)}
+ volume = {99},
+ pages = {45-56},
+ url = {http://www.bioinfo.de/isb/gcb99/talks/chevreux/main.html}
+ }
+
diff -r e59904c855ae -r 63ebe9726219 tools/mira3/tool_dependencies.xml
--- a/tools/mira3/tool_dependencies.xml Wed Apr 30 07:21:57 2014 -0400
+++ b/tools/mira3/tool_dependencies.xml Wed Aug 05 11:28:05 2015 -0400
@@ -1,27 +1,6 @@
-
-
-
- http://downloads.sourceforge.net/project/mira-assembler/MIRA/Older%20releases/V3.4.0/mira_3.4.1.1_prod_linux-gnu_x86_64_static.tar.bz2
-
- bin
- $INSTALL_DIR
-
-
- $INSTALL_DIR
-
-
-
-
-Downloads MIRA v3.4 from Sourceforge, requesting Bastien's precompiled binaries
-for 64bit Linux (x86_64). He also has binaries for 32bit Linux, which we could
-use once the Galaxy installation framework allow that kind of flexibility.
-
-http://chevreux.org/projects_mira.html
-http://sourceforge.net/projects/mira-assembler/
-
+
-