[Swift-commit] r5978 - SwiftApps/EpiSnp
wilde at ci.uchicago.edu
wilde at ci.uchicago.edu
Fri Oct 19 12:18:15 CDT 2012
Author: wilde
Date: 2012-10-19 12:18:04 -0500 (Fri, 19 Oct 2012)
New Revision: 5978
Added:
SwiftApps/EpiSnp/EPISNP1v41.gz
SwiftApps/EpiSnp/cf
SwiftApps/EpiSnp/chroms.tgz
SwiftApps/EpiSnp/episnp.swift
SwiftApps/EpiSnp/epiwrap.sh
SwiftApps/EpiSnp/sites.xml
SwiftApps/EpiSnp/tc
SwiftApps/EpiSnp/trait.dat
Log:
Initial EpiSnp code
Added: SwiftApps/EpiSnp/EPISNP1v41.gz
===================================================================
(Binary files differ)
Property changes on: SwiftApps/EpiSnp/EPISNP1v41.gz
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: SwiftApps/EpiSnp/cf
===================================================================
--- SwiftApps/EpiSnp/cf (rev 0)
+++ SwiftApps/EpiSnp/cf 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,360 @@
+sites.file=${swift.home}/etc/sites.xml
+tc.file=${swift.home}/etc/tc.data
+
+#
+# The host name of the submit machine is used by GRAM as a callback
+# address to report the status of submitted jobs. In general, Swift
+# can automatically detect the host name of the local machine.
+# However, if the machine host name is improperly configured or if
+# it does not represent a valid DNS entry, certain services (such as
+# GRAM) will not be able to send job status notifications back to
+# the client. The value of this property can be an IP address.
+#
+# Format:
+# hostname=string
+#
+
+
+#hostname=localhost
+
+#
+# A TCP port range can be specified to restrict the ports on which GRAM
+# callback services are started. This is likely needed if your submit
+# host is behind a firewall, in which case the firewall should be
+# configured to allow incoming connections on ports in the range.
+#
+# Format:
+# tcp.port.range=start,end
+#
+
+#tcp.port.range=50000,50100
+
+#
+# false - means an error will be immediately reported and cause the
+# workflow to abort. At this time remote jobs that are already
+# running will not be canceled
+# true - means that Swift will try to do as much work as possible and
+# report all errors encountered at the end. However, "errors"
+# here only applies to job execution errors. Certain errors
+# that are related to the Swift implementation (should such
+# errors occur) will still be reported eagerly.
+#
+# Default: false
+#
+lazy.errors=false
+
+#
+# What algorithm to use for caching of remote files. LRU (as in what
+# files to purge) is the only implementation right now. One can set
+# a target size (in bytes) for a host by using the swift:storagesize
+# profile for a host in sites.xml
+#
+# Default: LRU
+#
+caching.algorithm=LRU
+
+#
+# true - generate a provenance graph in .dot format (Swift will
+# choose a random file name)
+# false - do not generate a provenance graph
+# <filename> - generate a provenange graph in the give file name
+#
+# Default: false
+#
+pgraph=false
+
+
+#
+# graph properties for the provenance graph (.dot specific)
+#
+# Default: splines="compound", rankdir="TB"
+#
+pgraph.graph.options=splines="compound", rankdir="TB"
+
+
+#
+# node properties for the provenance graph (.dot specific)
+#
+# Default: color="seagreen", style="filled"
+#
+pgraph.node.options=color="seagreen", style="filled"
+
+#
+# true - clustering of small jobs is enabled. Clustering works in the
+# following way: If a job is clusterable (meaning that it has the
+# GLOBUS::maxwalltime profile specified in tc.data and its value
+# is less than the value of the "clustering.min.time" property) it will
+# be put in a clustering queue. The queue is processed at intervals
+# specified by the "clustering.queue.delay" property. The processing
+# of the clustering queue consists of selecting compatible jobs and
+# grouping them in clusters whose max wall time does not exceed twice
+# the value of the "clustering.min.time" property. Two or more jobs are
+# considered compatible if they share the same site and do not have
+# conflicting profiles (e.g. different values for the same environment
+# variable).
+# false - clustering of small jobs is disabled.
+#
+# Default: false
+#
+clustering.enabled=false
+
+
+#
+# <seconds> - the intervals at which the clustering queue is processed
+#
+# Default: 4
+#
+clustering.queue.delay=4
+
+#
+# <seconds> - the threshold time for clustering
+#
+# Default: 60
+#
+clustering.min.time=60
+
+#
+# Kickstart is a useful tool that can be used to gather various information
+# about a remote process. Before it can be used it must be installed on the
+# remote site and the corresponding entry be set in the sites file.
+# This option allows controlling of how Swift uses Kickstart. The following
+# values are possible:
+# false - do not use Kickstart
+# true - use Kickstart. If a job is scheduled on a site that does not have
+# Kickstart installed, that job will fail.
+# maybe - Use Kickstart if installed (i.e. the entry is present in the sites
+# file)
+#
+# Default: maybe
+#
+
+kickstart.enabled=maybe
+
+#
+# Indicates when Kickstart records should be fetched from the remote site:
+# true - always transfer Kickstart records if Kickstart was used (see
+# kickstart.enabled)
+# false - only transfer Kickstart records if the job fails
+#
+# Default: false
+#
+
+kickstart.always.transfer=false
+
+#
+# Indicates when wrapper logs should be fetched from the remote site:
+# true - always transfer wrapper logs
+# false - only transfer wrapper logs if the job fails
+#
+# Default: false
+#
+
+wrapperlog.always.transfer=false
+
+###########################################################################
+# Throttling options #
+###########################################################################
+#
+# For the throttling parameters, valid values are either a positive integer
+# or "off" (without the quotes).
+#
+
+#
+# Limits the number of concurrent submissions for a workflow instance. This
+# throttle only limits the number of concurrent tasks (jobs) that are being
+# sent to sites, not the total number of concurrent jobs that can be run.
+# The submission stage in GRAM is one of the most CPU expensive stages (due
+# mostly to the mutual authentication and delegation). Having too many
+# concurrent submissions can overload either or both the submit host CPU
+# and the remote host/head node causing degraded performance.
+#
+# Default: 4
+#
+
+throttle.submit=4
+#throttle.submit=off
+
+#
+# Limits the number of concurrent submissions for any of the sites Swift will
+# try to send jobs to. In other words it guarantees that no more than the
+# value of this throttle jobs sent to any site will be concurrently in a state
+# of being submitted.
+#
+# Default: 2
+#
+
+throttle.host.submit=2
+#throttle.host.submit=off
+
+#
+# The Swift scheduler has the ability to limit the number of concurrent jobs
+# allowed on a site based on the performance history of that site. Each site
+# is assigned a score (initially 1), which can increase or decrease based
+# on whether the site yields successful or faulty job runs. The score for a
+# site can take values in the (0.1, 100) interval. The number of allowed jobs
+# is calculated using the following formula:
+# 2 + score*throttle.score.job.factor
+# This means a site will always be allowed at least two concurrent jobs and
+# at most 2 + 100*throttle.score.job.factor. With a default of 4 this means
+# at least 2 jobs and at most 402.
+#
+# Default: 4
+#
+
+throttle.score.job.factor=0.2
+#throttle.score.job.factor=off
+
+
+#
+# Limits the total number of concurrent file transfers that can happen at any
+# given time. File transfers consume bandwidth. Too many concurrent transfers
+# can cause the network to be overloaded preventing various other signalling
+# traffic from flowing properly.
+#
+# Default: 4
+#
+
+throttle.transfers=4
+#throttle.transfers=off
+
+# Limits the total number of concurrent file operations that can happen at any
+# given time. File operations (like transfers) require an exclusive connection
+# to a site. These connections can be expensive to establish. A large number
+# of concurrent file operations may cause Swift to attempt to establish many
+# such expensive connections to various sites. Limiting the number of concurrent
+# file operations causes Swift to use a small number of cached connections and
+# achieve better overall performance.
+#
+# Default: 8
+#
+
+throttle.file.operations=8
+#throttle.file.operations=off
+
+# Indicates whether the working directory on the remote site should be
+# left intact even when the workflow completes successfully. This can be
+# used to inspect the site working directory for debugging purposes.
+#
+# Default: false
+#
+
+sitedir.keep=false
+
+# number of time a job will be retried if it fails (giving a maximum of
+# 1 + execution.retries attempts at execution)
+#
+
+execution.retries=2
+
+
+# Enables/disables replication. Replication is used to deal with jobs sitting
+# in batch queues for abnormally large amounts of time. If replication is enabled
+# and certain conditions are met, Swift creates and submits replicas of jobs, and
+# allows multiple instances of a job to compete.
+#
+
+replication.enabled=false
+
+# If replication is enabled, this value specifies the minimum time, in seconds,
+# a job needs to be queued in a batch queue in order to be considered for
+# replication
+#
+
+replication.min.queue.time=60
+
+# The maximum number of replicas that Swift should attempt.
+
+replication.limit=3
+
+#
+# WARNING: This option is deprecated. Please use the hostname option.
+#
+# The IP address of the submit machine is used by GRAM as a callback
+# address to report the status of submitted jobs. In general, Swift
+# can automatically detect the IP address of the local machine.
+# However, if the machine has more than one network interface, Swift
+# will pick the first one, which may not be the right choice. It is
+# recommended that this property is set properly before attempting to
+# run jobs through GRAM.
+#
+# Format:
+# ip.address=x.y.z.w
+#
+
+#ip.address=127.0.0.1
+
+
+# Controls how Swift will communicate the result code of running user programs
+# from workers to the submit side. In files mode, a file
+# indicating success or failure will be created on the site shared filesystem.
+# In provider mode, the execution provider job status will
+# be used. Notably, GRAM2 does not return job statuses correctly, and so
+# provider mode will not work with GRAM2. With other
+# providers, it can be used to reduce the amount of filesystem access compared
+# to files mode.
+#
+# status.mode=files
+
+# Controls how swift will supply parameters to the remote wrapper script.
+# 'args' mode will pass parameters on the command line
+# 'files' mode will pass parameters through an additional input file
+#
+# valid values: args, files
+# Default: files
+#
+# wrapper.parameter.mode=args
+
+# Determines if Swift remote wrappers will be executed by specifying an
+# absolute path, or a path relative to the job initial working directory
+#
+# valid values: absolute, relative
+# wrapper.invocation.mode=absolute
+
+#
+# Limits the number of concurrent iterations that each foreach statement
+# can have at one time. This conserves memory for swift programs that
+# have large numbers of iterations (which would otherwise all be executed
+# in parallel).
+#
+# Default: 1024
+#
+
+foreach.max.threads=16384
+
+# controls whether the log file will contain provenance information
+# enabling this will increase the size of log files, sometimes
+# significantly.
+
+provenance.log=false
+
+# Controls whether file staging is done by swift or by the execution
+# provider. If set to false, the standard swift staging mechanism is
+# used. If set to true, swift does not stage files. Instead, the
+# execution provider is instructed to stage files in and out.
+#
+# Provider staging is experimental.
+#
+# When enabled, and when coasters are used as an execution provider,
+# a staging mechanism can be selected for each site
+# using the swift:stagingMethod site profile in sites.xml. The
+# following is a list of accepted mechanisms:
+#
+# * file: Staging is done from a filesystem accessible to the
+# coaster service (typically running on the head node)
+# * proxy: Staging is done from a filesystem accessible to the
+# client machine that swift is running on, and is proxied
+# through the coaster service
+# * sfs: (short for "shared filesystem") Staging is done by
+# copying files to and from a filesystem accessible
+# by the compute node (such as an NFS or GPFS mount).
+
+
+use.provider.staging=false
+
+# Changed settings:
+
+wrapperlog.always.transfer=true
+sitedir.keep=true
+execution.retries=0
+lazy.errors=false
+status.mode=provider
Added: SwiftApps/EpiSnp/chroms.tgz
===================================================================
(Binary files differ)
Property changes on: SwiftApps/EpiSnp/chroms.tgz
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: SwiftApps/EpiSnp/episnp.swift
===================================================================
--- SwiftApps/EpiSnp/episnp.swift (rev 0)
+++ SwiftApps/EpiSnp/episnp.swift 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,24 @@
+type file;
+
+app (file fig, file sig, file log) episnp (file wrapper, file exec, file trait, file chroms, int nSingles, int nPairs)
+{
+ sh @wrapper @exec @trait @chroms nSingles nPairs @log @fig @sig;
+}
+
+file epiwrapper<"epiwrap.sh">;
+file epiexec<"EPISNP1v41.gz">;
+file epitrait <"trait.dat">;
+file epichroms<"chroms.tgz">;
+
+file logout[]<simple_mapper; location="output", prefix="episnp.",suffix=".out">;
+file figout[]<simple_mapper; location="output", prefix="single_locus_fig.",suffix=".out">;
+file sigout[]<simple_mapper; location="output", prefix="single_locus_sig.",suffix=".out">;
+
+int nRuns = @toint(@arg("nRuns","1"));
+
+foreach incr, i in [0:nRuns-1] {
+ (figout[i], sigout[i], logout[i]) = episnp(epiwrapper, epiexec, epitrait, epichroms, 1000+i, 10000+i);
+}
+
+
+
Added: SwiftApps/EpiSnp/epiwrap.sh
===================================================================
--- SwiftApps/EpiSnp/epiwrap.sh (rev 0)
+++ SwiftApps/EpiSnp/epiwrap.sh 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,56 @@
+#! /bin/sh
+
+# called from swift app cmd: sh @wrapper @exec @trait @chroms nSingles nPairs @epiout @fig @sig;
+
+exec=$1
+trait=$2
+chroms=$3
+nSingles=$4
+nPairs=$5
+epiout=$6
+figout=$7
+sigout=$8
+
+echo $0: exec=$exec trait=$trait chroms=$chroms nSingles=$nSingles nPairs=$nPairs figout=$figout sigout=$sigout
+
+cp $exec episnp.gz
+gunzip episnp
+chmod +x episnp
+
+tar zxf $chroms
+
+# FIXME: make # chrNN.dat files below depend on # files in input tarball
+
+cat >parameter.dat <<END
+0
+1 # number of traits
+6 # starting position of traits in the trait file
+4 1 2 # number of column for gender information and codes for male and female
+9999 # code for missing traits, non-genetic factors and covariables
+1654 # number of individuals
+0 # number of non-genetic factors
+0 # positions of the non-genetic factors
+0 # number of covariables
+0 # positions of covariables in the trait file
+6 # number of chromosomes
+30 # sex chromosome number
+1 # 1: 0=A1A1, 1=A1A2, 2=A2A2 and others=missing used for coding; 2: A1/A1, A1/A2 and A2/A2 used for coding, 0/0 used for missing
+2 # starting position of SNPs in the SNP data file
+1500 chr01.dat
+1200 chr02.dat
+1300 chr03.dat
+1400 chr04.dat
+1500 chr05.dat
+1600 chr06.dat
+trait.dat # file name of the phenotype data
+$nSingles # number of most significant results for single SNP tests to be printed in the output file
+$nPairs # number of most significant results for pairwise tests to be printed in the output file
+END
+
+./episnp >& episnp.out
+
+mv episnp.out $epiout
+mv single_locus_fig.out $figout
+mv single_locus_sig.out $sigout
+
+
Property changes on: SwiftApps/EpiSnp/epiwrap.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: SwiftApps/EpiSnp/sites.xml
===================================================================
--- SwiftApps/EpiSnp/sites.xml (rev 0)
+++ SwiftApps/EpiSnp/sites.xml 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,7 @@
+<config>
+ <pool handle="localhost">
+ <execution provider="local"/>
+ <filesystem provider="local"/>
+ <workdirectory >/home/wilde/swiftwork</workdirectory>
+ </pool>
+</config>
Added: SwiftApps/EpiSnp/tc
===================================================================
--- SwiftApps/EpiSnp/tc (rev 0)
+++ SwiftApps/EpiSnp/tc 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,46 @@
+#This is the transformation catalog.
+#
+#It comes pre-configured with a number of simple transformations with
+#paths that are likely to work on a linux box. However, on some systems,
+#the paths to these executables will be different (for example, sometimes
+#some of these programs are found in /usr/bin rather than in /bin)
+#
+#NOTE WELL: fields in this file must be separated by tabs, not spaces; and
+#there must be no trailing whitespace at the end of each line.
+#
+# sitename transformation path INSTALLED platform profiles
+localhost sh /bin/sh INSTALLED INTEL32::LINUX null
+localhost echo /bin/echo INSTALLED INTEL32::LINUX null
+localhost cat /bin/cat INSTALLED INTEL32::LINUX null
+localhost ls /bin/ls INSTALLED INTEL32::LINUX null
+localhost grep /bin/grep INSTALLED INTEL32::LINUX null
+localhost sort /bin/sort INSTALLED INTEL32::LINUX null
+localhost paste /bin/paste INSTALLED INTEL32::LINUX null
+localhost pwd /bin/pwd INSTALLED INTEL32::LINUX null
+#
+ranger cat /bin/cat INSTALLED INTEL32::LINUX null
+abe cat /bin/cat INSTALLED INTEL32::LINUX null
+qb cat /bin/cat INSTALLED INTEL32::LINUX null
+firefly cat /bin/cat INSTALLED INTEL32::LINUX null
+teraport cat /bin/cat INSTALLED INTEL32::LINUX null
+pbs cat /bin/cat null null null
+ssh cat /bin/cat null null null
+rssh scat /home/wilde/swift/lab/scat null null null
+sico cat /bin/cat null null null
+sico scat /home/wilde/swift/lab/scat null null null
+
+#########
+
+crush cat /bin/cat null null null
+thwomp cat /bin/cat null null null
+stomp cat /bin/cat null null null
+crank cat /bin/cat null null null
+steamroller cat /bin/cat null null null
+grind cat /bin/cat null null null
+churn cat /bin/cat null null null
+trounce cat /bin/cat null null null
+thrash cat /bin/cat null null null
+vanquish cat /bin/cat null null null
+octagon cat /bin/cat null null null
+octopus cat /bin/cat null null null
+triumph cat /bin/cat null null null
Added: SwiftApps/EpiSnp/trait.dat
===================================================================
--- SwiftApps/EpiSnp/trait.dat (rev 0)
+++ SwiftApps/EpiSnp/trait.dat 2012-10-19 17:18:04 UTC (rev 5978)
@@ -0,0 +1,1655 @@
+Ind_ID Father Mather Sex V1 V2
+39365164 2514957 251496 2 -0.024249451 -0.008311192
+39365317 2458842 245884 2 -0.024640478 -0.005954723
+41613317 39069784 3906978 2 -0.023986114 0.007279951
+41613948 2605219 260522 2 -0.024424976 -0.007425483
+41616376 2619125 261913 2 -0.024352501 -0.010362572
+41616727 2599307 259931 2 -0.024452038 0.001807755
+42212025 39069784 3906978 2 -0.024628581 -0.003051996
+42213207 2599307 259931 2 -0.024624802 -0.012352243
+42450432 2605219 260522 2 -0.024499769 0.005495207
+42451542 2605219 260522 2 -0.024233538 -0.000559442
+43151963 2617409 261741 2 -0.024759088 -0.02081158
+43151964 34497515 3449752 2 -0.024632632 -0.007996824
+35119306 2394422 239442 2 -0.024014885 -0.009605842
+35096810 2394422 239442 2 -0.02397682 -0.015134982
+35386984 2332434 233243 2 -0.023795731 -0.005213932
+35611311 2332434 233243 2 -0.023518193 -0.007434283
+35895508 2607954 260795 2 -0.024326758 0.000192713
+35909665 2607954 260795 2 -0.024243873 -0.010231569
+37110737 2467939 246794 2 -0.024228158 -0.02267634
+37575919 2470808 247081 2 -0.024473009 -0.015076175
+37578280 2455053 245505 2 -0.024376582 -0.018000156
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+35119307 2394422 239442 2 -0.024043743 -0.010964472
+35386974 2314284 231428 2 -0.024150982 0.005478606
+35611317 2332434 233243 2 -0.023911567 -0.011803293
+35611322 2406276 240628 2 -0.025036246 -0.013471531
+35895515 2607954 260795 2 -0.023727397 -0.012250855
+36185763 2405465 240547 2 -0.024247355 -0.015618297
+37110738 2455053 245505 2 -0.024126405 -0.017026646
+37110739 2467939 246794 2 -0.024069778 -0.025611017
+37575965 2470808 247081 2 -0.024644203 0.001016539
+37576591 2470808 247081 2 -0.024747204 -0.008613882
+37799919 2455053 245505 2 -0.024385097 -0.012735086
+37800348 2455053 245505 2 -0.02430688 -0.022906221
+38110432 2473557 247356 2 -0.023783453 -0.024644736
+38111366 2455053 245505 2 -0.024350111 -0.011380525
+38881855 2514957 251496 2 -0.023924431 -0.011209712
+38882200 2439114 243911 2 -0.024517323 0.041103817
+17489567 2325626 232563 2 -0.024259562 -0.015291021
+17489581 2273408 227341 2 -0.023869636 -0.009449827
+38883130 2439114 243911 2 -0.02563748 0.028095182
+35386979 2314284 231428 2 -0.024442422 -0.003221223
+35386980 2539707 253971 2 -0.023764491 0.002567522
+35620206 2406276 240628 2 -0.024391167 -0.002295695
+35885153 2368204 236820 2 -0.024267205 0.004146435
+36742899 2607954 260795 2 -0.024221113 -0.001477216
+36742900 2406276 240628 2 -0.02423881 -0.013845755
+37110742 2455053 245505 2 -0.024553128 -0.004100016
+37334022 2467939 246794 2 -0.025203233 -0.009441317
+37577276 2473557 247356 2 -0.024455149 -0.023657146
+40329970 2467939 246794 2 -0.02487377 -0.015460641
+38109866 2455053 245505 2 -0.024137743 -0.013280453
+38110308 2470808 247081 2 -0.024740747 -0.013095291
+35386976 2314284 231428 2 -0.024579693 0.007921365
+35386977 2539707 253971 2 -0.023915301 -0.008467072
+35611324 2406276 240628 2 -0.02557557 -0.015669468
+36180489 2406276 240628 2 -0.023918287 -0.013042656
+36180491 2368204 236820 2 -0.024031324 0.003209519
+37110740 2473557 247356 2 -0.024529858 -0.018880574
+37110741 2467939 246794 2 -0.024706971 -0.009741066
+37576809 2473557 247356 2 -0.024537301 -0.015773812
+37577239 2467939 246794 2 -0.024448675 -0.017685566
+38109669 2455053 245505 2 -0.024381287 -0.014825508
+38109846 2470808 247081 2 -0.02423583 -0.013147149
+39366258 2458842 245884 2 -0.024679269 0.001836519
+39725746 2563198 256320 2 -0.024415448 -0.019712114
+41615419 2619125 261913 2 -0.02517064 -0.010118711
+41615420 2619125 261913 2 -0.024256751 -0.009587081
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\ No newline at end of file
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