BiopetCommandLineFunctionTrait.scala 8.33 KB
Newer Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
/**
 * Biopet is built on top of GATK Queue for building bioinformatic
 * pipelines. It is mainly intended to support LUMC SHARK cluster which is running
 * SGE. But other types of HPC that are supported by GATK Queue (such as PBS)
 * should also be able to execute Biopet tools and pipelines.
 *
 * Copyright 2014 Sequencing Analysis Support Core - Leiden University Medical Center
 *
 * Contact us at: sasc@lumc.nl
 *
 * A dual licensing mode is applied. The source code within this project that are
 * not part of GATK Queue is freely available for non-commercial use under an AGPL
 * license; For commercial users or users who do not want to follow the AGPL
 * license, please contact us to obtain a separate license.
 */
16
17
18
package nl.lumc.sasc.biopet.core

import java.io.File
Peter van 't Hof's avatar
Peter van 't Hof committed
19
import nl.lumc.sasc.biopet.core.config.Configurable
Peter van 't Hof's avatar
Peter van 't Hof committed
20
21
import org.broadinstitute.gatk.queue.QException
import org.broadinstitute.gatk.queue.function.CommandLineFunction
22
23
import org.broadinstitute.gatk.utils.commandline.{ Input, Argument }
import scala.sys.process.{ Process, ProcessLogger }
24
import scala.util.matching.Regex
25
26
import java.io.FileInputStream
import java.security.MessageDigest
27

Peter van 't Hof's avatar
Peter van 't Hof committed
28
/** Biopet command line trait to auto check executable and cluster values */
29
trait BiopetCommandLineFunctionTrait extends CommandLineFunction with Configurable {
Peter van 't Hof's avatar
Peter van 't Hof committed
30
  analysisName = configName
bow's avatar
bow committed
31
32

  @Input(doc = "deps", required = false)
33
  var deps: List[File] = Nil
bow's avatar
bow committed
34

35
36
  var threads = 0
  val defaultThreads = 1
bow's avatar
bow committed
37

38
39
40
41
42
43
44
  var vmem: Option[String] = config("vmem")
  var defaultCoreMemory: Double = 1.0
  var vmemFactor: Double = config("vmem_factor", default =
    this match {
      case _: BiopetJavaCommandLineFunction => 2.5
      case _                                => 1.5
    })
Peter van 't Hof's avatar
Peter van 't Hof committed
45
  var executable: String = _
bow's avatar
bow committed
46

Peter van 't Hof's avatar
Peter van 't Hof committed
47
48
49
50
  /**
   * Can override this method. This is executed just before the job is ready to run.
   * Can check on run time files from pipeline here
   */
Peter van 't Hof's avatar
Peter van 't Hof committed
51
  protected[core] def beforeCmd {}
Peter van 't Hof's avatar
Peter van 't Hof committed
52

Peter van 't Hof's avatar
Peter van 't Hof committed
53
  /** Can override this method. This is executed after the script is done en queue starts to generate the graph */
54
  protected[core] def beforeGraph {}
Peter van 't Hof's avatar
Peter van 't Hof committed
55

Peter van 't Hof's avatar
Peter van 't Hof committed
56
  /** Set default output file, threads and vmem for current job */
57
  override def freezeFieldValues() {
58
    preProcesExecutable
59
    beforeGraph
60
    if (jobOutputFile == null) jobOutputFile = new File(firstOutput.getAbsoluteFile.getParent, "." + firstOutput.getName + "." + configName + ".out")
bow's avatar
bow committed
61

62
63
    if (threads == 0) threads = getThreads(defaultThreads)
    if (threads > 1) nCoresRequest = Option(threads)
bow's avatar
bow committed
64

65
66
67
    val coreMemory: Double = config("core_memory", default = defaultCoreMemory)
    if (memoryLimit.isEmpty) memoryLimit = Some(coreMemory * threads)

Peter van 't Hof's avatar
Peter van 't Hof committed
68
    if (vmem.isEmpty) {
69
70
71
      val vmemTemp = defaultCoreMemory * vmemFactor

      vmem = Some(vmemTemp + "G")
72
    }
Peter van 't Hof's avatar
Peter van 't Hof committed
73
    if (vmem.isDefined) jobResourceRequests :+= "h_vmem=" + vmem.get
74
    jobName = configName + ":" + (if (firstOutput != null) firstOutput.getName else jobOutputFile)
bow's avatar
bow committed
75

76
77
    super.freezeFieldValues()
  }
bow's avatar
bow committed
78

79
80
81
  /** can override this value is executable may not be converted to CanonicalPath */
  val executableToCanonicalPath = true

Peter van 't Hof's avatar
Peter van 't Hof committed
82
83
84
  /**
   * Checks executable. Follow full CanonicalPath, checks if it is existing and do a md5sum on it to store in job report
   */
85
  protected[core] def preProcesExecutable {
86
87
88
89
90
91
92
93
94
95
    if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
      try if (executable != null) {
        if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable)) {
          val oldExecutable = executable
          val buffer = new StringBuffer()
          val cmd = Seq("which", executable)
          val process = Process(cmd).run(ProcessLogger(buffer.append(_)))
          if (process.exitValue == 0) {
            executable = buffer.toString
            val file = new File(executable)
96
97
            if (executableToCanonicalPath) executable = file.getCanonicalPath
            else executable = file.getAbsolutePath
98
          } else {
99
            BiopetQScript.addError("executable: '" + executable + "' not found, please check config")
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
          }
          BiopetCommandLineFunctionTrait.executableCache += oldExecutable -> executable
          BiopetCommandLineFunctionTrait.executableCache += executable -> executable
        } else {
          executable = BiopetCommandLineFunctionTrait.executableCache(executable)
        }

        if (!BiopetCommandLineFunctionTrait.executableMd5Cache.contains(executable)) {
          val is = new FileInputStream(executable)
          val cnt = is.available
          val bytes = Array.ofDim[Byte](cnt)
          is.read(bytes)
          is.close()
          val temp = MessageDigest.getInstance("MD5").digest(bytes).map("%02X".format(_)).mkString.toLowerCase
          BiopetCommandLineFunctionTrait.executableMd5Cache += executable -> temp
        }
      } catch {
        case ioe: java.io.IOException => logger.warn("Could not use 'which', check on executable skipped: " + ioe)
118
119
      }
    }
120
121
    val md5 = BiopetCommandLineFunctionTrait.executableMd5Cache.get(executable)
    addJobReportBinding("md5sum_exe", md5.getOrElse("None"))
122
  }
bow's avatar
bow committed
123

Peter van 't Hof's avatar
Peter van 't Hof committed
124
  /** executes checkExecutable method and fill job report */
125
  final protected def preCmdInternal {
126
    preProcesExecutable
bow's avatar
bow committed
127

128
    beforeCmd
bow's avatar
bow committed
129

Peter van 't Hof's avatar
Peter van 't Hof committed
130
131
    addJobReportBinding("cores", nCoresRequest match {
      case Some(n) if n > 0 => n
132
      case _                => 1
Peter van 't Hof's avatar
Peter van 't Hof committed
133
    })
134
    addJobReportBinding("version", getVersion)
135
  }
bow's avatar
bow committed
136

Peter van 't Hof's avatar
Peter van 't Hof committed
137
  /** Command to get version of executable */
138
  protected def versionCommand: String = null
Peter van 't Hof's avatar
Peter van 't Hof committed
139
140

  /** Regex to get version from version command output */
141
  protected val versionRegex: Regex = null
Peter van 't Hof's avatar
Peter van 't Hof committed
142
143
144
145
146

  /** Allowed exit codes for the version command */
  protected val versionExitcode = List(0)

  /** Executes the version command */
147
148
  private def getVersionInternal: Option[String] = {
    if (versionCommand == null || versionRegex == null) return None
149
    val exe = new File(versionCommand.trim.split(" ")(0))
150
    if (!exe.exists()) return None
151
152
    val stdout = new StringBuffer()
    val stderr = new StringBuffer()
153
154
155
156
    def outputLog = "Version command: \n" + versionCommand +
      "\n output log: \n stdout: \n" + stdout.toString +
      "\n stderr: \n" + stderr.toString
    val process = Process(versionCommand).run(ProcessLogger(stdout append _ + "\n", stderr append _ + "\n"))
157
    if (!versionExitcode.contains(process.exitValue)) {
158
      logger.warn("getVersion give exit code " + process.exitValue + ", version not found \n" + outputLog)
159
      return None
160
    }
161
    for (line <- stdout.toString.split("\n") ++ stderr.toString.split("\n")) {
bow's avatar
bow committed
162
      line match {
163
        case versionRegex(m) => return Some(m)
Peter van 't Hof's avatar
Peter van 't Hof committed
164
        case _               =>
165
166
      }
    }
167
    logger.warn("getVersion give a exit code " + process.exitValue + " but no version was found, executable correct? \n" + outputLog)
168
    return None
169
  }
bow's avatar
bow committed
170

Peter van 't Hof's avatar
Peter van 't Hof committed
171
  /** Get version from cache otherwise execute the version command  */
172
  def getVersion: Option[String] = {
Peter van 't Hof's avatar
Peter van 't Hof committed
173
    if (!BiopetCommandLineFunctionTrait.executableCache.contains(executable))
174
      preProcesExecutable
175
176
177
178
179
180
    if (!BiopetCommandLineFunctionTrait.versionCache.contains(versionCommand))
      getVersionInternal match {
        case Some(version) => BiopetCommandLineFunctionTrait.versionCache += versionCommand -> version
        case _             =>
      }
    BiopetCommandLineFunctionTrait.versionCache.get(versionCommand)
Peter van 't Hof's avatar
Peter van 't Hof committed
181
182
  }

Peter van 't Hof's avatar
Peter van 't Hof committed
183
184
185
186
187
  /**
   * Get threads from config
   * @param default default when not found in config
   * @return number of threads
   */
bow's avatar
bow committed
188
189
190
  def getThreads(default: Int): Int = {
    val maxThreads: Int = config("maxthreads", default = 8)
    val threads: Int = config("threads", default = default)
191
192
193
    if (maxThreads > threads) return threads
    else return maxThreads
  }
bow's avatar
bow committed
194

Peter van 't Hof's avatar
Peter van 't Hof committed
195
196
197
198
199
200
  /**
   * Get threads from config
   * @param default default when not found in config
   * @param module Module when this is difrent from default
   * @return number of threads
   */
bow's avatar
bow committed
201
202
203
  def getThreads(default: Int, module: String): Int = {
    val maxThreads: Int = config("maxthreads", default = 8, submodule = module)
    val threads: Int = config("threads", default = default, submodule = module)
204
205
206
207
    if (maxThreads > threads) return threads
    else return maxThreads
  }
}
Peter van 't Hof's avatar
Peter van 't Hof committed
208

Peter van 't Hof's avatar
Peter van 't Hof committed
209
/** stores global caches */
Peter van 't Hof's avatar
Peter van 't Hof committed
210
211
212
object BiopetCommandLineFunctionTrait {
  import scala.collection.mutable.Map
  private val versionCache: Map[String, String] = Map()
213
  private[core] val executableMd5Cache: Map[String, String] = Map()
214
  private val executableCache: Map[String, String] = Map()
215
}