1. EMBL-EBI, programmatically - take a REST from manual searching: Sequence analysis tools
Web Production Team
Anna Foix
Joon Lee

2. Contents EBI Tools RESTful Clients Where to get the clients
Show you how to run the clients
How to use a simple pipeline manually
Where to get help and support

3. RESTful Clients
RESTful Web Services enable applications and services to run over the web
Access to these happens using URIs
Provide a uniform interface. Clients exist in a variety of programming languages
Resources are decoupled from their representation and can be access through a broad variety of formats such as HTML, XML, text, JSON, etc.
Users no longer need to maintain applications and databases

4. EBI Tools Clients
There are many categories of Web Services in bioinformatics (e.g. sequence similarity, multiple sequence alignments, data retrieval, etc.)
Ready to use Clients exist in Python, Perl, Java, Ruby, C, C#...and can be obtained here!
At you will find a lot of information about our Web Services

5. Where to get the clients

6. How to run the clients
How to run NCBI Blast
How to run EMBOSS Water

7. Stitching things together
Using a shell script
Using CWL (Common Workflow Language)

8. How to run the clients as a workflow
Running blastp against swissprot
Getting the IDs from blastp
Fetching sequenes using dbfetch
Running Clustal Omega
Running Simple phylogency

9. Workflow by a shell script
../ncbiblast/ncbiblast_lwp.pl -- $ --program blastp --database uniprotkb_swissprot --stype protein --sequence $inputSeq --outformat ids --outfile $$ cat $$.ids.txt | head -5 | sed 's/SP\://g;'| tr '\n' ',' | ../dbfetch_lwp.pl fetchBatch uniprot - fasta raw >> $$.fasta ../clustalo/clustalo_lwp.pl -- $ --sequence …….. ../simple_phylogeny/simple_phylogeny_lwp.pl -- $ --sequence $$.aln-clustal.clustal --outformat tree -- outfile $$

10. Workflow by CWL script
steps: ncbiblast_step: run: '../ncbiblast/ncbiblast.cwl’ dbfetch: run: '../dbfetch/dbfetch.cwl‘ in: accessions: ncbiblast_step/ids out: [aligned_sequences] clustalo_step: run: '../clustalo/clustalo.cwl‘ in: sequences: dbfetch/aligned_sequences out: [clustalo_out]

11. NCBI BLAST CWL
inputs: command: type: File inputBinding: default: class: File location: ncbiblast_lwp.pl type: string inputBinding: prefix: -- default:
program: type: string inputBinding: prefix: --program default: 'blastp‘
database: type: string inputBinding: prefix: --database default: 'uniprotkb_swissprot‘
type: type: string inputBinding: prefix: --stype default: 'protein'

12. Clustal Omega CWL
inputs: command: type: File inputBinding: default: class: File location: clustalo_lwp.pl type: string inputBinding: prefix: -- default:
outformat: type: string inputBinding: prefix: --outformat default: 'aln-clustal’
sequences: type: File inputBinding: prefix: -- sequence
outputs: clustalo_out: type: stdout

13. More help and support https://www.ebi.ac.uk/Tools/webservices