[Swift-commit] r8368 - SwiftApps/ematter/galaxy
ketan at ci.uchicago.edu
ketan at ci.uchicago.edu
Wed Jan 21 10:22:50 CST 2015
Author: ketan
Date: 2015-01-21 10:22:49 -0600 (Wed, 21 Jan 2015)
New Revision: 8368
Added:
SwiftApps/ematter/galaxy/smeagol_lead.swift
SwiftApps/ematter/galaxy/swiftsmeagol_lead.py
Modified:
SwiftApps/ematter/galaxy/smeagol0.xml
SwiftApps/ematter/galaxy/smeagol_lead.xml
SwiftApps/ematter/galaxy/smeagoln.xml
Log:
smeagol tool
Modified: SwiftApps/ematter/galaxy/smeagol0.xml
===================================================================
--- SwiftApps/ematter/galaxy/smeagol0.xml 2015-01-20 19:41:32 UTC (rev 8367)
+++ SwiftApps/ematter/galaxy/smeagol0.xml 2015-01-21 16:22:49 UTC (rev 8368)
@@ -1,102 +1,57 @@
-<tool id="swiftjumpdsp" name="dsp swift">
+<tool id="swiftsmeagol_lead" name="smeagol lead swift">
+
<!--
ToDo:
- 1. Option if the counter should be an argument, first one or last one.
- 2. Option to add files (in Galaxy dataset format) as arguments. These files then be added to Swift app as arguments.
- 3. Allow the tool to select another tool and run it.
- 4. Allow user to add more than one resource to run a job for load balancing.
- 5. Add ability to run Swift/T.
- 6. Let the localhost option be selected by default
+ 1.
-->
- <description>A Galaxy tool to run Dsp parameter sweeps via Swift foreach parallel construct</description>
+ <description>A Galaxy tool to run the smeagol lead tool via Swift</description>
+
<command interpreter="python">
- swiftjumpdsp.py
- "${inlocation}"
- "${a}"
- "${n}"
- "${p}"
- "${I}"
+ swiftsmeagol_lead.py
+ "${_aupsf}"
+ "${_ausicpsf}"
+ "${_inputfdf}"
+ "${_opsf}"
+ "${_osicpsf}"
+ "${_tipsf}"
+ "${_tisicpsf}"
+ "${_au3dm}"
+ "${_au3hst}"
+ "${_bulklft}"
+ "${_bulkrgt}"
+ "${_out}"
"${local_or_compute}"
- "${resloc}"
- "${outlist}"
- "${outlogfile}"
</command>
<inputs>
- <param name="inlocation" size="60" type="text" label="inlocation" value="/home/ketan/SwiftApps/dsp-swift/dcap" help="Enter the path of the directory containing input data, eg. /home/ketan/farmer" />
- <param name="a" size="30" type="text" label="aval" value="1" help="Enter the value of a" />
- <param name="n" size="30" type="text" label="nval" value="1" help="Enter the value of n" />
- <param name="p" size="30" type="text" label="pval" value="1" help="Enter the value of p" />
- <param name="I" size="30" type="text" label="Ival" value="10" help="Enter the value of I" />
+ <param name="_aupsf" size="30" type="data" label="aupsf" help="Select data for aupsf" />
+ <param name="_ausicpsf" size="30" type="data" label="ausicpsf" help="Select data for ausicpsf" />
+ <param name="_inputfdf" size="30" type="data" label="inputfdf" help="Select data for inputfdf" />
+ <param name="_opsf" size="30" type="data" label="opsf" help="Select data for opsf" />
+ <param name="_osicpsf" size="30" type="data" label="osicpsf" help="Select data for osicpsf" />
+ <param name="_tipsf" size="30" type="data" label="tipsf" help="Select data for tipsf" />
+ <param name="_tisicpsf" size="30" type="data" label="tisicpsf" help="Select data for tisicpsf" />
+
<param name="local_or_compute" type="select" display="radio" label="choose target execution location">
<option value="local" selected="true">local</option>
<option value="compute">compute</option>
</param>
- <param name="resloc" size="60" type="text" label="Location for results" value="/tmp/outdir" help="Enter the path to a directory to put results in, eg. /tmp/outdir"/>
</inputs>
<outputs>
- <data format="txt" name="outlist" type="data" label="Output List" />
- <data format="txt" name="outlogfile" type="data" label="Swift Progress" />
+ <data format="txt" name="_au3dm" type="data" label="au3 DM output" />
+ <data format="txt" name="_au3hst" type="data" label="au3 HST output" />
+ <data format="txt" name="_bulklft" type="data" label="bulk left output" />
+ <data format="txt" name="_bulkrgt" type="data" label="bulk right output" />
+ <data format="txt" name="_out" type="data" label="smeagol lead output" />
</outputs>
+
<help>
-**What is this?**
-A tool to run dsp in parallel parameter sweeps.
-
-**What it does?**
-
-Runs dsp in parallel over a user provided input dataset and parameters.
-
-**How does it do?**
-
-The user provides input to the tool which is then delivered to the
-underlying Swift script. The script is then invoked on local/login or
-compute nodes as selected by the user. Once the tool has run, the output is
-produced in the directory location provided by the user.
-
More description to come.
</help>
</tool>
-/* ==
-This is a Swift workflow script for the ematter application. The script contains the following parts:
-
--- A one-line type declaration
--- App function definitions
--- Input files and variables definitions
--- Output files definitions
--- Invocation of app functions
-== */
-
-type file;
-
-
-/* == App function definitions == */
-
-/* == Lammps app definition == */
-app (file _dump) lammps_app (file _in, file _geo, file _eam)
-{
- lammps "-in" @_in;
-}
-
-/* == Pizza app definition == */
-app (file _xyz) pizza_app (file _pizza_src, file _dump)
-{
- python @_pizza_src @_dump @_xyz;
-}
-
-/* == Pasta app definition == */
-app (file _fdf) pasta_app (file _pasta_src, file _xyz, file _fdf_tmp)
-{
- bash @_pasta_src @_xyz @_fdf_tmp @_fdf;
-}
-
-/* ==
-smeagol lead inputs
-Au.psf Au.sic.psf input.fdf
-O.psf O.sic.psf Ti.psf Ti.sic.psf
-== */
-
+<!--
/* == Smeagol lead app definition == */
app (file _au3dm, file _au3hst,
file _bulklft, file _bulkrgt,
@@ -108,148 +63,4 @@
mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
}
-/* ==
-smeagol transport V0 inputs
-Au3.DM Au3.HST Au.psf
-Au.sic.psf bulklft.DAT bulkrgt.DAT
-input.fdf O.psf O.sic.psf
-Ti.psf Ti.sic.psf
-== */
-
-/* == Smeagol transport V0 app definition == */
-app (file _tio2auhm, file _tio2audm,
- file _out) smeagol_v0_app ( file _au3dm, file _au3hst, file _aupsf,
- file _ausicpsf, file _bulklft, file _bulkrgt,
- file _inputfdf, file _opsf, file _osicpsf,
- file _tipsf, file _tisicpsf )
-{
- mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
-}
-
-/* == Generate fdfs app definition == */
-app (file _fdf) gen_fdf(file _genfdf_src, float _r, file _infdf)
-{
- bash @_genfdf_src _r @_infdf stdout=@_fdf;
-}
-
-/* == Smeagol transport Vn app definition == */
-app (file _trc_out, file _out) smeagol_vn_app ( file _au3dm,
- file _au3hst, file _aupsf,
- file _ausicpsf, file _bulklft,
- file _bulkrgt, file _inputfdf,
- file _opsf, file _osicpsf,
- file _tipsf, file _tisicpsf )
-{
- mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
-}
-
-/* == Input files definitions: Make sure these files are available in the current directory == */
-file lammps_in <"in.lammps">;
-file lammps_geo <"AuTiO.geo">;
-file lammps_eam <"Au_u3.eam">;
-
-file fdf_leads<"input_leads.fdf">;
-file fdf_v0<"input_t0.fdf">;
-
-file aupsf <"Au.psf">;
-file ausicpsf <"Au.sic.psf">;
-file opsf <"O.psf">;
-file osicpsf <"O.sic.psf">;
-file tipsf <"Ti.psf">;
-file tisicpsf <"Ti.sic.psf">;
-
-file pizza_src<"lastlammpsdump2xyz.py">;
-file pasta_src<"pasta">;
-file genfdf_src<"genfdf">;
-
-/* == Output files definitions == */
-file xyz <"forsmeagol.xyz">;
-file lammps_dump <"lammps.dump">;
-file fdf_proc<"input_proc.fdf">;
-
-file smeagol_lead_out <"smeagol_out/smeagol.lead.out">;
-file smeagol_transport_out<"smeagol_out/smeagol.transport.out">;
-file au3dm <"Au3.DM">;
-file au3hst <"Au3.HST">;
-
-file bulklft <"bulklft.DAT">;
-file bulkrgt <"bulkrgt.DAT">;
-
-file tio2auhm<"TiO2Au.HM">;
-file tio2audm<"TiO2Au.DM">;
-
-/* == unused
-file[] smeagol_transport_outn<simple_mapper; location="smeagol_out",
- prefix="smeagol.", suffix=".out">;
-file[] fdf_proc_vn;
-== */
-
-
-/* == unused for now
-float Vstart=0.1; //== Change this value to change the starting voltage ==
-float Vend=1.0; //== Change this value to change the ending voltage ==
-float Vstep=0.1;
-== */
-
-string Vs[]=["0.1","0.2","0.3","0.4","0.5","0.6","0.7","0.8","0.9","1.0"];
-
-/* == End files and variable declaration == */
-
-
-/* == Invocation of apps == */
-
-/* == Invoke lammps == */
-(lammps_dump) = lammps_app (lammps_in, lammps_geo, lammps_eam);
-
-/* == Invoke pizza == */
-(xyz) = pizza_app(pizza_src, lammps_dump);
-
-
-/* == Invoke smeagol lead == */
-(au3dm, au3hst,
- bulklft, bulkrgt,
- smeagol_lead_out) = smeagol_lead_app (aupsf, ausicpsf, fdf_leads,
- opsf, osicpsf,
- tipsf, tisicpsf);
-
-
-/* == Invoke smeagol transport V0 == */
-(tio2auhm, tio2audm,
- smeagol_transport_out) = smeagol_v0_app(au3dm, au3hst,
- aupsf, ausicpsf,
- bulklft, bulkrgt,
- fdf_v0, opsf, osicpsf,
- tipsf, tisicpsf);
-
-/* == Invoke pasta == */
-(fdf_proc) = pasta_app(pasta_src, xyz, fdf_v0);
-
-
-/* ==
-In a parallel 'foreach' loop, invoke gen_fdf and smeagol for the n V calculations
-== */
-
-foreach v,i in Vs
-{
-/* == generate fdfs for different voltages == */
-string fdfname = strcat("input_", v, ".fdf");
-file fdf_proc_vn <single_file_mapper; file=fdfname>;
-
-fdf_proc_vn = gen_fdf(genfdf_src, toFloat(v), fdf_proc);
-
-string outname = strcat("smeagol_out/bias_", v, ".out");
-file smeagol_transport_outn <single_file_mapper; file=outname>;
-
-file smeagol_trc_out <single_file_mapper; file=strcat("0.TiO2Au_", v, ".TRC")>;
-
-(smeagol_trc_out, smeagol_transport_outn) = smeagol_vn_app(au3dm, au3hst,
- aupsf, ausicpsf,
- bulklft, bulkrgt,
- fdf_proc_vn, opsf,
- osicpsf, tipsf,
- tisicpsf);
-
-
-}
-
-
+-->
Added: SwiftApps/ematter/galaxy/smeagol_lead.swift
===================================================================
--- SwiftApps/ematter/galaxy/smeagol_lead.swift (rev 0)
+++ SwiftApps/ematter/galaxy/smeagol_lead.swift 2015-01-21 16:22:49 UTC (rev 8368)
@@ -0,0 +1,35 @@
+type file;
+
+
+app (file _au3dm, file _au3hst,
+ file _bulklft, file _bulkrgt,
+ file _out) smeagol_lead_app (file _aupsf, file _ausicpsf,
+ file _inputfdf, file _opsf,
+ file _osicpsf, file _tipsf,
+ file _tisicpsf)
+{
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
+}
+
+file aupsf <single_file_mapper; file=arg("aupsf")>;
+file ausicpsf <single_file_mapper; file=arg("ausicpsf")>;
+file inputfdf <single_file_mapper; file=arg("inputfdf")>;
+file opsf <single_file_mapper; file=arg("opsf")>;
+file osicpsf <single_file_mapper; file=arg("osicpsf")>;
+file tipsf <single_file_mapper; file=arg("tipsf")>;
+file tisicpsf <single_file_mapper; file=arg("tisicpsf")>;
+file au3dm <single_file_mapper; file=arg("au3dm")>;
+file au3hst <single_file_mapper; file=arg("au3hst")>;
+file bulklft <single_file_mapper; file=arg("bulklft")>;
+file bulkrgt <single_file_mapper; file=arg("bulkrgt")>;
+file out <single_file_mapper; file=arg("out")>;
+
+
+(file au3dm, file au3hst,
+ file bulklft, file bulkrgt,
+ file out) = smeagol_lead_app (file aupsf, file ausicpsf,
+ file inputfdf, file opsf,
+ file osicpsf, file tipsf,
+ file tisicpsf);
+
+
Modified: SwiftApps/ematter/galaxy/smeagol_lead.xml
===================================================================
--- SwiftApps/ematter/galaxy/smeagol_lead.xml 2015-01-20 19:41:32 UTC (rev 8367)
+++ SwiftApps/ematter/galaxy/smeagol_lead.xml 2015-01-21 16:22:49 UTC (rev 8368)
@@ -1,67 +1,57 @@
-<tool id="swiftjumpdsp" name="dsp swift">
+<tool id="swiftsmeagol_lead" name="smeagol lead swift">
+
<!--
ToDo:
- 1. Option if the counter should be an argument, first one or last one.
- 2. Option to add files (in Galaxy dataset format) as arguments. These files then be added to Swift app as arguments.
- 3. Allow the tool to select another tool and run it.
- 4. Allow user to add more than one resource to run a job for load balancing.
- 5. Add ability to run Swift/T.
- 6. Let the localhost option be selected by default
+ 1.
-->
- <description>A Galaxy tool to run Dsp parameter sweeps via Swift foreach parallel construct</description>
+ <description>A Galaxy tool to run the smeagol lead tool via Swift</description>
+
<command interpreter="python">
- swiftjumpdsp.py
- "${inlocation}"
- "${a}"
- "${n}"
- "${p}"
- "${I}"
+ swiftsmeagol_lead.py
+ "${_aupsf}"
+ "${_ausicpsf}"
+ "${_inputfdf}"
+ "${_opsf}"
+ "${_osicpsf}"
+ "${_tipsf}"
+ "${_tisicpsf}"
+ "${_au3dm}"
+ "${_au3hst}"
+ "${_bulklft}"
+ "${_bulkrgt}"
+ "${_out}"
"${local_or_compute}"
- "${resloc}"
- "${outlist}"
- "${outlogfile}"
</command>
<inputs>
- <param name="inlocation" size="60" type="text" label="inlocation" value="/home/ketan/SwiftApps/dsp-swift/dcap" help="Enter the path of the directory containing input data, eg. /home/ketan/farmer" />
- <param name="a" size="30" type="text" label="aval" value="1" help="Enter the value of a" />
- <param name="n" size="30" type="text" label="nval" value="1" help="Enter the value of n" />
- <param name="p" size="30" type="text" label="pval" value="1" help="Enter the value of p" />
- <param name="I" size="30" type="text" label="Ival" value="10" help="Enter the value of I" />
+ <param name="_aupsf" size="30" type="data" label="aupsf" help="Select data for aupsf" />
+ <param name="_ausicpsf" size="30" type="data" label="ausicpsf" help="Select data for ausicpsf" />
+ <param name="_inputfdf" size="30" type="data" label="inputfdf" help="Select data for inputfdf" />
+ <param name="_opsf" size="30" type="data" label="opsf" help="Select data for opsf" />
+ <param name="_osicpsf" size="30" type="data" label="osicpsf" help="Select data for osicpsf" />
+ <param name="_tipsf" size="30" type="data" label="tipsf" help="Select data for tipsf" />
+ <param name="_tisicpsf" size="30" type="data" label="tisicpsf" help="Select data for tisicpsf" />
+
<param name="local_or_compute" type="select" display="radio" label="choose target execution location">
<option value="local" selected="true">local</option>
<option value="compute">compute</option>
</param>
- <param name="resloc" size="60" type="text" label="Location for results" value="/tmp/outdir" help="Enter the path to a directory to put results in, eg. /tmp/outdir"/>
</inputs>
<outputs>
- <data format="txt" name="outlist" type="data" label="Output List" />
- <data format="txt" name="outlogfile" type="data" label="Swift Progress" />
+ <data format="txt" name="_au3dm" type="data" label="au3 DM output" />
+ <data format="txt" name="_au3hst" type="data" label="au3 HST output" />
+ <data format="txt" name="_bulklft" type="data" label="bulk left output" />
+ <data format="txt" name="_bulkrgt" type="data" label="bulk right output" />
+ <data format="txt" name="_out" type="data" label="smeagol lead output" />
</outputs>
+
<help>
-**What is this?**
-A tool to run dsp in parallel parameter sweeps.
-
-**What it does?**
-
-Runs dsp in parallel over a user provided input dataset and parameters.
-
-**How does it do?**
-
-The user provides input to the tool which is then delivered to the
-underlying Swift script. The script is then invoked on local/login or
-compute nodes as selected by the user. Once the tool has run, the output is
-produced in the directory location provided by the user.
-
More description to come.
</help>
</tool>
-
-type file;
-
-
+<!--
/* == Smeagol lead app definition == */
app (file _au3dm, file _au3hst,
file _bulklft, file _bulkrgt,
@@ -73,3 +63,4 @@
mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
}
+-->
Modified: SwiftApps/ematter/galaxy/smeagoln.xml
===================================================================
--- SwiftApps/ematter/galaxy/smeagoln.xml 2015-01-20 19:41:32 UTC (rev 8367)
+++ SwiftApps/ematter/galaxy/smeagoln.xml 2015-01-21 16:22:49 UTC (rev 8368)
@@ -1,75 +1,66 @@
-<tool id="swiftjumpdsp" name="dsp swift">
+<tool id="swiftsmeagol_lead" name="smeagol lead swift">
+
<!--
ToDo:
- 1. Option if the counter should be an argument, first one or last one.
- 2. Option to add files (in Galaxy dataset format) as arguments. These files then be added to Swift app as arguments.
- 3. Allow the tool to select another tool and run it.
- 4. Allow user to add more than one resource to run a job for load balancing.
- 5. Add ability to run Swift/T.
- 6. Let the localhost option be selected by default
+ 1.
-->
- <description>A Galaxy tool to run Dsp parameter sweeps via Swift foreach parallel construct</description>
+ <description>A Galaxy tool to run the smeagol lead tool via Swift</description>
+
<command interpreter="python">
- swiftjumpdsp.py
- "${inlocation}"
- "${a}"
- "${n}"
- "${p}"
- "${I}"
+ swiftsmeagol_lead.py
+ "${_aupsf}"
+ "${_ausicpsf}"
+ "${_inputfdf}"
+ "${_opsf}"
+ "${_osicpsf}"
+ "${_tipsf}"
+ "${_tisicpsf}"
+ "${_au3dm}"
+ "${_au3hst}"
+ "${_bulklft}"
+ "${_bulkrgt}"
+ "${_out}"
"${local_or_compute}"
- "${resloc}"
- "${outlist}"
- "${outlogfile}"
</command>
<inputs>
- <param name="inlocation" size="60" type="text" label="inlocation" value="/home/ketan/SwiftApps/dsp-swift/dcap" help="Enter the path of the directory containing input data, eg. /home/ketan/farmer" />
- <param name="a" size="30" type="text" label="aval" value="1" help="Enter the value of a" />
- <param name="n" size="30" type="text" label="nval" value="1" help="Enter the value of n" />
- <param name="p" size="30" type="text" label="pval" value="1" help="Enter the value of p" />
- <param name="I" size="30" type="text" label="Ival" value="10" help="Enter the value of I" />
+ <param name="_aupsf" size="30" type="data" label="aupsf" help="Select data for aupsf" />
+ <param name="_ausicpsf" size="30" type="data" label="ausicpsf" help="Select data for ausicpsf" />
+ <param name="_inputfdf" size="30" type="data" label="inputfdf" help="Select data for inputfdf" />
+ <param name="_opsf" size="30" type="data" label="opsf" help="Select data for opsf" />
+ <param name="_osicpsf" size="30" type="data" label="osicpsf" help="Select data for osicpsf" />
+ <param name="_tipsf" size="30" type="data" label="tipsf" help="Select data for tipsf" />
+ <param name="_tisicpsf" size="30" type="data" label="tisicpsf" help="Select data for tisicpsf" />
+
<param name="local_or_compute" type="select" display="radio" label="choose target execution location">
<option value="local" selected="true">local</option>
<option value="compute">compute</option>
</param>
- <param name="resloc" size="60" type="text" label="Location for results" value="/tmp/outdir" help="Enter the path to a directory to put results in, eg. /tmp/outdir"/>
</inputs>
<outputs>
- <data format="txt" name="outlist" type="data" label="Output List" />
- <data format="txt" name="outlogfile" type="data" label="Swift Progress" />
+ <data format="txt" name="_au3dm" type="data" label="au3 DM output" />
+ <data format="txt" name="_au3hst" type="data" label="au3 HST output" />
+ <data format="txt" name="_bulklft" type="data" label="bulk left output" />
+ <data format="txt" name="_bulkrgt" type="data" label="bulk right output" />
+ <data format="txt" name="_out" type="data" label="smeagol lead output" />
</outputs>
+
<help>
-**What is this?**
-A tool to run dsp in parallel parameter sweeps.
-
-**What it does?**
-
-Runs dsp in parallel over a user provided input dataset and parameters.
-
-**How does it do?**
-
-The user provides input to the tool which is then delivered to the
-underlying Swift script. The script is then invoked on local/login or
-compute nodes as selected by the user. Once the tool has run, the output is
-produced in the directory location provided by the user.
-
More description to come.
</help>
</tool>
-
-type file;
-
-
-/* == Smeagol transport Vn app definition == */
-app (file _trc_out, file _out) smeagol_vn_app ( file _au3dm,
- file _au3hst, file _aupsf,
- file _ausicpsf, file _bulklft,
- file _bulkrgt, file _inputfdf,
- file _opsf, file _osicpsf,
- file _tipsf, file _tisicpsf )
+<!--
+/* == Smeagol lead app definition == */
+app (file _au3dm, file _au3hst,
+ file _bulklft, file _bulkrgt,
+ file _out) smeagol_lead_app (file _aupsf, file _ausicpsf,
+ file _inputfdf, file _opsf,
+ file _osicpsf, file _tipsf,
+ file _tisicpsf)
{
- mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
+ mpiexec "/home/heinonen/smeagol-1.2-Feb-2014/smeagol-1.2_blues/Src/smeagol-1.2_csg" stdin=@_inputfdf stdout=@_out;
}
+-->
Added: SwiftApps/ematter/galaxy/swiftsmeagol_lead.py
===================================================================
--- SwiftApps/ematter/galaxy/swiftsmeagol_lead.py (rev 0)
+++ SwiftApps/ematter/galaxy/swiftsmeagol_lead.py 2015-01-21 16:22:49 UTC (rev 8368)
@@ -0,0 +1,79 @@
+#!/usr/bin/env python
+
+"""
+This is the Swift driver for Galaxy. It receives inputs from the Swift
+Galaxy tool and depending on the options specified, builds a
+canonical Swift/K or Swift/T script and runs over specified computational
+environment.
+
+swiftsmeagol_lead.py
+ "${_aupsf}"
+ "${_ausicpsf}"
+ "${_inputfdf}"
+ "${_opsf}"
+ "${_osicpsf}"
+ "${_tipsf}"
+ "${_tisicpsf}"
+ "${_au3dm}"
+ "${_au3hst}"
+ "${_bulklft}"
+ "${_bulkrgt}"
+ "${_out}"
+ "${local_or_compute}"
+
+"""
+
+import subprocess
+import sys
+import os
+import distutils.spawn
+import traceback
+import fnmatch
+import re
+from os.path import expanduser
+
+def genargs(args):
+ for a in args:
+ yield a
+
+def main():
+ myargs = genargs(sys.argv)
+ try:
+ this=next(myargs)
+ aupsf = next(myargs)
+ ausicpsf = next(myargs)
+ inputfdf = next(myargs)
+ opsf = next(myargs)
+ osicpsf = next(myargs)
+ tipsf = next(myargs)
+ tisicpsf = next(myargs)
+ au3dm = next(myargs)
+ au3hst = next(myargs)
+ bulklft = next(myargs)
+ bulkrgt = next(myargs)
+ out = next(myargs)
+ local_or_compute = next(myargs)
+ except:
+ traceback.print_exc()
+ sys.exit(1)
+
+ homedir = expanduser("~")
+
+ baseloc = homedir+"/SwiftApps/ematter/galaxy"
+
+ #which swift
+ swift = homedir+"/swift-0.95/cog/modules/swift/dist/swift-svn/bin/swift"
+ swiftargs="-aupsf="+aupsf+" -ausicpsf="+ausicpsf+" -inputfdf="+inputfdf+" -opsf="+opsf+" -osicpsf="+osicpsf+" -tipsf="+tipsf+" -tisicpsf="+tisicpsf+" -au3dm="+au3dm+" -au3hst="+au3hst+" -bulklft="+bulklft+" -bulkrgt="+bulkrgt+" -out="+out
+
+ siteval=baseloc+"/sites.local.xml"
+
+ if local_or_compute == "compute":
+ siteval=baseloc+"/sites.blues.xml"
+
+ #Invocation
+ exitcode=subprocess.check_call([swift, "-sites.file", siteval, "-tc.file", baseloc+"/apps", "-config", baseloc+"/cf", baseloc+"/smeagol_lead.swift", swiftargs])
+ #print exitcode
+
+if __name__=='__main__':
+ main()
+
Property changes on: SwiftApps/ematter/galaxy/swiftsmeagol_lead.py
___________________________________________________________________
Added: svn:executable
+ *
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