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ComparativeGenomicsToolkit / cactus

Official home of genome aligner based upon notion of Cactus graphs
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cactus-hal2maf installation issue #1360

Open hopehealey opened 2 months ago

hopehealey commented 2 months ago

Cactus installed correctly on my computer (and works), but cactus-hal2maf did not install. Has anyone had this issue before? How can I install cactus-hal2maf?

$ cactus usage: cactus [-h] [--config PATH] [--logCritical] [--logError] [--logWarning] [--logDebug] [--logInfo] [--logOff] [--logLevel {Critical,Error,Warning,Debug,Info,critical,error,warning,debug,info,CRITICAL,ERROR,WARNING,DEBUG,INFO}] [--logFile LOGFILE] [--rotatingLogging] [--workDir PATH] [--coordinationDir PATH] [--noStdOutErr] [--stats] [--clean {always,onError,never,onSuccess}] [--cleanWorkDir {always,onError,never,onSuccess}] [--clusterStats [OPT_PATH]] [--restart] [--batchSystem {aws_batch,single_machine,grid_engine,lsf,mesos,slurm,torque,htcondor,kubernetes}] [--disableHotDeployment] [--disableAutoDeployment DISABLEAUTODEPLOYMENT] [--maxJobs MAX_JOBS] [--maxLocalJobs MAX_LOCAL_JOBS] [--manualMemArgs] [--runLocalJobsOnWorkers] [--coalesceStatusCalls] [--statePollingWait STATEPOLLINGWAIT] [--batchLogsDir BATCH_LOGS_DIR] [--awsBatchRegion AWS_BATCH_REGION] [--awsBatchQueue AWS_BATCH_QUEUE] [--awsBatchJobRoleArn AWS_BATCH_JOB_ROLE_ARN] [--scale SCALE] [--dont_allocate_mem | --allocate_mem] [--symlinkImports BOOL] [--moveOutputs BOOL] [--caching BOOL] [--provisioner {aws,gce,None}] [--nodeTypes NODETYPES] [--maxNodes INT[,INT...]] [--minNodes INT[,INT...]] [--targetTime INT] [--betaInertia FLOAT] [--scaleInterval INT] [--preemptibleCompensation FLOAT] [--nodeStorage INT] [--nodeStorageOverrides NODETYPE:NODESTORAGE[,NODETYPE:NODESTORAGE...]] [--metrics BOOL] [--assumeZeroOverhead BOOL] [--maxServiceJobs INT] [--maxPreemptibleServiceJobs INT] [--deadlockWait INT] [--deadlockCheckInterval INT] [--defaultMemory DEFAULTMEMORY] [--defaultCores FLOAT] [--defaultDisk INT] [--defaultAccelerators ACCELERATOR[,ACCELERATOR...]] [--defaultPreemptible [BOOL]] [--maxCores INT] [--maxMemory INT] [--maxDisk INT] [--retryCount INT] [--enableUnlimitedPreemptibleRetries BOOL] [--doubleMem BOOL] [--maxJobDuration INT] [--rescueJobsFrequency INT] [--maxLogFileSize MAXLOGFILESIZE] [--writeLogs [OPT_PATH]] [--writeLogsGzip [OPT_PATH]] [--writeLogsFromAllJobs BOOL] [--writeMessages PATH] [--realTimeLogging REALTIMELOGGING] [--disableChaining BOOL] [--disableJobStoreChecksumVerification BOOL] [--sseKey PATH] [--setEnv NAME=VALUE or NAME] [--servicePollingInterval FLOAT] [--forceDockerAppliance BOOL] [--statusWait INT] [--disableProgress BOOL] [--debugWorker] [--disableWorkerOutputCapture] [--badWorker FLOAT] [--badWorkerFailInterval FLOAT] [--configFile CONFIGFILE] [--root ROOT] [--latest] [--containerImage CONTAINERIMAGE] [--binariesMode {docker,local,singularity}] [--gpu [GPU]] [--lastzCores LASTZCORES] [--lastzMemory LASTZMEMORY] [--consCores CONSCORES] [--consMemory CONSMEMORY] [--intermediateResultsUrl INTERMEDIATERESULTSURL] [--skipPreprocessor] [--maxOutgroups MAXOUTGROUPS] [--chromInfo CHROMINFO] jobStore seqFile outputHal cactus: error: the following arguments are required: jobStore, seqFile, outputHal

$ cactus-hal2maf bash: cactus-hal2maf: command not found

glennhickey commented 2 months ago

That's strange. You may want to try installing again and looking out for any error messages... These tools should all end up in the same place:

ls -l cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus*
-rwxr-xr-x 1 hickey cgl 295 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus
-rwxr-xr-x 1 hickey cgl 283 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-align
-rwxr-xr-x 1 hickey cgl 295 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-align-batch
-rwxr-xr-x 1 hickey cgl 283 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-blast
-rwxr-xr-x 1 hickey cgl 287 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-graphmap
-rwxr-xr-x 1 hickey cgl 292 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-graphmap-join
-rwxr-xr-x 1 hickey cgl 293 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-graphmap-split
-rwxr-xr-x 1 hickey cgl 286 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-hal2chains
-rwxr-xr-x 1 hickey cgl 283 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-hal2maf
-rwxr-xr-x 1 hickey cgl 286 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-maf2bigmaf
-rwxr-xr-x 1 hickey cgl 288 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-minigraph
-rwxr-xr-x 1 hickey cgl 288 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-pangenome
-rwxr-xr-x 1 hickey cgl 291 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-prepare
-rwxr-xr-x 1 hickey cgl 301 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-prepare-toil
-rwxr-xr-x 1 hickey cgl 297 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-preprocess
-rwxr-xr-x 1 hickey cgl 285 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-refmap
-rwxr-xr-x 1 hickey cgl 296 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-terra-helper
-rwxr-xr-x 1 hickey cgl 293 Apr  4 12:20 cactus-bin-v2.8.1/venv-cactus-v2.8.1/bin/cactus-update-prepare