HPRC Galaxy Maroon, Silver, Kaiser

HPRC GalaxyMaroon, Silver, KaiserTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Your HPRC Galaxy Username and Password Your HPRC Galaxy login is the same as your TAMUaccount NetID and password Both state of Texas law and TAMU regulationsprohibit the sharing and/or illegal use of computerpasswords and accounts Don’t write down passwords Don’t choose easy to guess/crack passwordsTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

For More Help.Website:Email:Telephone:Visit us in person:Texas A&M Universityhprc.tamu.eduhelp@hprc.tamu.edu(979) 845-0219Henderson Hall, Room 114AHigh Performance Research Computinghttps://hprc.tamu.edu

What is the Galaxy Project? Texas A&M UniversityHigh Performance Research Computingusegalaxy.orgpublic Galaxy instancereproducible workflowshared data andworkflowsmany popularbioinformatic tools areavailableno programmingknowledge requiredtry usegalaxy.org tosee if Galaxy is a goodfit for your projecthttps://hprc.tamu.edu

Galaxy 101https://galaxyproject.org/learnThere are many tutorialsavailable with example inputdata and step by step analysisfor various topicsTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

HPRC GalaxyMaroon, Silver, KaiserTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

HPRC Silver GalaxyThe same tutorials found atgalaxyproject.org/learn canbe accessed here TAMU HPRC Galaxy instanceAvailable to TAMU students,staff and xas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

HPRC Galaxy Noteshprc.tamu.edu/wiki/SW:GalaxyTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

New Galaxy Features1.You can easily switch to an older software version2.You can add tools to your favorites to easily locate later3.4.Disk quota enforced for all usersa. all users begin with 1TB disk quotab. request an increase if needed but permanently deleted nonessential files firstc. compressed (gzipped) file format is supportedTutorials are easy to follow along without leaving Silver Galaxy5.Job Resource Parameters available for cores, memory and job timetoolssupportingmulti-coreprocessingTexas A&M Universitytoolssupportingsingle-coreprocessingHigh Performance Research Computinghttps://hprc.tamu.edu

Silver Galaxy Try Galaxy at usegalaxy.org to see if it appropriate for your projectGetting Access to HPRC Silver Galaxy Available to Texas A&M students, staff and faculty with a NetIDand an HPRC account Apply for an HPRC account first https://hprc.tamu.edu/apply Then send an email request for a Silver Galaxy account help@hprc.tamu.edu Need to use VPN when connecting to Galaxy from off campus Login to Silver Galaxy using your TAMU NetID and passwordRead the Galaxy Usage Notes https://hprc.tamu.edu/wiki/SW:GalaxyThere are no backups of users’ Galaxy filesTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Look for Additionally Available Toolshttps://toolshed.g2.bx.psu.eduTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Uploading files to your Galaxy HistoryTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Get Data into Your Galaxy Historyupload button Upload files 2GB in size using Galaxy web interface select local file on your computer to upload paste URL address of any size file Can retrieve data from external websites directly intoyour Galaxy history with ‘Get Data’ tools UCSC, BioMart, Ratmine, .Texas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

HTTP URL Upload File 2GB in size or Direct Paste1paste http URL32Texas A&M University4High Performance Research Computinghttps://hprc.tamu.edu

Uploading a 2GB size file to Silver Galaxy Files larger than 2GB should be copied using ftp instead of the upload buttonThere are three options for uploading files via ftpa. Use the sftp command in a Unix terminal on your Mac or Linux desktopb. Copy files from Terra SCRATCH directory to ftp directory using sftp on Terrac. Use sftp on BitVise on your Windows desktop to copy from your desktop to Terra After copying file to the Galaxy ftp directory, go to Galaxy 'upload file' interface inGalaxy to see your ftp transferred file (next ng Files .3E 2GB via FTP to Maroon GalaxyTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Add Your FTP Uploaded 2GB size File to Your History132Texas A&M University4High Performance Research Computinghttps://hprc.tamu.edu

FTP Upload File 2GB size directly to History via URL1paste ftp URL324You can URL upload a 2GB sized file if the URL is an ftp siteTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Copy a file between historiesview all historiesHistorydisk usageTotal disk usage.Mouse over the'Using' icon to seetotalDrag and drop files from onehistory to another to copy a filewithout duplicating the original fileand increasing your disk usageThe History disk usage reflects anincrease based on the file size but youroverall disk usage does not increaseTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

File and History ManagementTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Automatic detection of fastqsanger format forfastq UploadsGalaxy will automatically detectfastqsanger format and setformat attribute accordingly.There is no need to run theFastq Groomer tool on this file.Texas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Galaxy File Formats Many Galaxy tools require fastqsanger not just fastq Galaxy now auto detects and assigns fastqsanger format FastQC tool will check fastq format of a fastq file MiSeq, HiSeq, NextSeq, NovaSeq all use 1.8 Texas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Permanently Delete Nonessential Filesdeletes files from disk and reduces your Galaxy disk usagedelete fileshow deleted filespermanently delete filehide deleted filesNotice how History disk usage went down only after permanently deleting fileTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Check Your HPRC SUs BalanceYou can also change your default HPRC project accountIf you are unable to run the HPRC SU balance tool thenyou most likely need to renew your HPRC accountTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

History Dividerjob with 2output filesUsed to add a spacer between outputfiles of distinct job so you can seewhich files were created by each jobRun the History Divider tool betweenjobsjob with 2output filesjob with 1output fileTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Shared Data LibrariesFiles can be added to a ‘Data Library’ which you can share with your colleagues.Send a request to the HPRC helpdesk if you would like a Data Library for your groupTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Debugging Failed JobsTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Failed to Queue Job Make sure you have enough SUs to runthe job My HPRC SU BalanceMake sure your account has beenrenewed for current fiscal yearTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Failed Job: walltime limit reached Configure the job to use more TimeTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Failed Job: memory limit reached Configure the job to use more MemoryorTexas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

See Logs of Failed Jobs1.2.3.4.Check error log by clicking onthe bug iconClick the information iconCheck the stderr file linkCheck the stdout file link4If you are unable to determine thecause of the error after reviewing allthe log messages, send an email tothe HPRC helpdesk with errorinformation Which Galaxy you are using History name History item numberTexas A&M University3High Performance Research Computing12https://hprc.tamu.edu

usegalaxy.org Exercise1.2.3.4.5.6.Add fasta file for S. cerevisiae chromosome I from genome.ucsc.edu to yourcurrent history and set the “Database/Build” attribute to the proper genomeassemblyRun the “Compute Sequence Length” tool to get length of chromosome IAdd fasta file for chromosome M from genome.ucsc.edu to your historyConcatenate the two files into one fileRun the “Compute Sequence Length” tool on the concatenated filePermanently delete the file you created in step 2.Texas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Thank you.Any questions?Texas A&M UniversityHigh Performance Research Computinghttps://hprc.tamu.edu

Silver Galaxy Try Galaxy at usegalaxy.org to see if it appropriate for your project Getting Access to HPRC Silver Galaxy Available to Texas A&M students, staff and faculty with a NetID and an HPRC account Apply for an HPRC account first https://hprc.tamu.edu/apply Then send an email request for a Silver Galaxy account