new files for v302 update

Author: NullModel

src/hg/encode3/eap/README

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+This the source code for the Encode Analysis Pipeline (EAP).  It is all available under the BSD 
+license as part of the ENCODE Project.
+
+The EAP is a system for running genomics pipelines implemented using mySQL, Parasol, and C.
+The C code is
+	eapDaemon - take anything in edwAnalysisJob table and feed it to Parasol
+	eapSchedule - set up edwAnalysisJob and edwAnalysisRun tables make output temp dirs
+	eapFinish - move stuff from output temp dirs into encode data warehouse
+	eapMonitor - look at how jobs are progressing through table and parasol.  
+	             If need be chill and kill steps gone awry.
+	eapAddSoftware - add a piece of software that is used by and tracked by the system
+	eapUpdateSoftware - Tell system about a new version of software
+	eapAddStep - add a new analysis step (something that processes files and generally
+	             creates other files, though there are also 'statistics only' steps.
+	eapMetaSync - still in development but meant to turn eap objects into JSON that gets
+	              sent to the metadatabase which responds with metaUuid we store in tables.
+There's also a few temporary programs:
+	eapRunAddJson - Creates JSON for ENCODED at Stanford, so that database can also
+	             track file relationships and steps.   This was just a second draft.
+		     It turns out we may well use a different approach.
+	eapToHub - Create a hub for DNAse hypersensitivity data calculated by EAP.  Just for
+	           demo.
+
+The overall process for making a new analysis is:
+1) Create an analysis step bash script that should start with the name "eap_run_" and belong
+   in the github shared with Stanford.
+2) Test the step on hgwdev installing anything needed, and keeping track of what is installed
+3) Test the step on ku, asking system admins to install anything needed to run it on that machine
+   or the associated cluster.
+4) Run eapAddSoftware to add any new software.  Do this on both hgwdev and encode-02
+5) Edit eapAddStep.c and make a new item in the step array for your step,  then run eapAddStep
+   on hgwdev and encode-02
+6) Edit eapSchedule.c to tell system in what circumstances to run the step.
+7) Schedule step on somewhere between 1 and 10 files using eapSchedule on encode-02
+8) Examine output directory in eapRun.tempDir and make sure it looks good.  It will be a subdir of
+   /hive/groups/encode/encode3/encodeAnalysisPipeline/tmp that starts with the step name.
+9) Edit eapFinish.c to tell system how to store results.
+10) Run eapFinish with -noClean flag (so you get a chance to correct bugs before it 
+    deletes the directory).
+11) Check database to make sure everything is good.
+12) Run eapSchedule with -step=yourStepName to tell system to do step on whole database on 
+    encode-02.
+13) Contact Jim before running step on encode-01 (the production site).

src/hg/encode3/eap/eapAddSoftware/eapAddSoftware.c

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+/* eapAddSoftware - Add a new software object. */
+
+/* Copyright (C) 2014 The Regents of the University of California 
+ * See README in this or parent directory for licensing information. */
+#include "common.h"
+#include "linefile.h"
+#include "hash.h"
+#include "options.h"
+#include "../../encodeDataWarehouse/inc/encodeDataWarehouse.h"
+#include "../../encodeDataWarehouse/inc/edwLib.h"
+#include "eapDb.h"
+#include "eapLib.h"
+
+void usage()
+/* Explain usage and exit. */
+{
+errAbort(
+  "eapAddSoftware - Add a new software object\n"
+  "usage:\n"
+  "   eapAddSoftware name version url email\n"
+  "options:\n"
+  "   -xxx=XXX\n"
+  );
+}
+
+/* Command line validation table. */
+static struct optionSpec options[] = {
+   {NULL, 0},
+};
+
+void eapAddSoftware(char *name, char *version, char *url, char *email)
+/* eapAddSoftware - Add a new software object. */
+{
+/* If we already have software by that name warn and return */
+struct sqlConnection *conn = eapConnectReadWrite();
+char query[1024];
+sqlSafef(query, sizeof(query), "select count(*) from eapSoftware where name='%s'", name);
+int existingCount = sqlQuickNum(conn, query);
+if (existingCount > 0)
+     {
+     warn("%s already exists in eapSoftware", name);
+     return;
+     }
+
+/* Add us. */
+sqlSafef(query, sizeof(query), "insert eapSoftware (name,url,email) values ('%s','%s','%s')",
+    name, url, email);
+sqlUpdate(conn, query);
+
+/* Find out executabe md5 */
+char path[PATH_LEN];
+eapPathForCommand(name, path);
+char md5[33];
+edwMd5File(path, md5);
+
+/* Add initial version as well */
+sqlSafef(query, sizeof(query), 
+    "insert eapSwVersion (software,version,md5,notes) values ('%s','%s','%s','%s')", 
+	name, version, md5, "Initial version tracked.");
+sqlUpdate(conn, query);
+}
+
+int main(int argc, char *argv[])
+/* Process command line. */
+{
+optionInit(&argc, argv, options);
+if (argc != 5)
+    usage();
+eapAddSoftware(argv[1], argv[2], argv[3], argv[4]);
+return 0;
+}

src/hg/encode3/eap/eapAddSoftware/makefile

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+kentSrc = ../../../..
+A = eapAddSoftware
+preMyLibs += ../lib/$(MACHTYPE)/eaplib.a ../../encodeDataWarehouse/lib/$(MACHTYPE)/edwlib.a ../../../../parasol/lib/$(MACHTYPE)/paralib.a
+include $(kentSrc)/inc/userApp.mk