Details
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Type:
New Feature
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Status: Closed (View Workflow)
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Priority:
Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: 9.1.6 Major Release
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Labels:None
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Story Points:3
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Epic Link:
-
Sprint:Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23, Fall 6 Nov 30 - Dec 11
Description
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.)
Modify this so that a user can specific the genome file using the "file" tag.
e.g.,
<file name="foo.2bit" reference="true"/>
and
<file name="https://example.com/foo.2bit" reference="True"/>
and
<file name="http://example.com/foo.2bit" reference="True"/>
For example 2bit files corresponding to various genomes, see:
This location contains multiple subdirectories for different genome versions. For example,
contains a file named mm10.2bit (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit) which contains the same data shown for IGB genome version M_musculus_Dec_2011.
Attachments
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Rank | Ranked higher |
| Rank | Ranked higher |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Sprint | Fall 1: 14 Sep - 25 Sep [ 103 ] | Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 103, 104 ] |
| Rank | Ranked higher |
| Description |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., <file name="foo.2bit genome_sequence="True"/> or <file name="https://example.com/foo.2bit" genome_sequence="True"/> |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., {code} <file name="foo.2bit" genome_sequence="True"/> {code} and {code} <file name="https://example.com/foo.2bit" genome_sequence="True"/> {code} and {code} <file name="http://example.com/foo.2bit" genome_sequence="True"/> {code} |
| Description |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., {code} <file name="foo.2bit" genome_sequence="True"/> {code} and {code} <file name="https://example.com/foo.2bit" genome_sequence="True"/> {code} and {code} <file name="http://example.com/foo.2bit" genome_sequence="True"/> {code} |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., {code} <file name="foo.2bit" reference="True"/> {code} and {code} <file name="https://example.com/foo.2bit" reference="True"/> {code} and {code} <file name="http://example.com/foo.2bit" reference="True"/> {code} For example 2bit files corresponding to various genomes, see: * http://hgdownload.soe.ucsc.edu/goldenPath This location contains multiple subdirectories for different genome versions. For example, * http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/ contains a file named mm10.2bit (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit) which contains the same data shown for IGB genome version M_musculus_Dec_2011. |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Description |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., {code} <file name="foo.2bit" reference="True"/> {code} and {code} <file name="https://example.com/foo.2bit" reference="True"/> {code} and {code} <file name="http://example.com/foo.2bit" reference="True"/> {code} For example 2bit files corresponding to various genomes, see: * http://hgdownload.soe.ucsc.edu/goldenPath This location contains multiple subdirectories for different genome versions. For example, * http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/ contains a file named mm10.2bit (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit) which contains the same data shown for IGB genome version M_musculus_Dec_2011. |
Currently, IGB assumes that the genome sequence for a genome version resides physically on the same server as the Quickload metadata files and that the genome version file is named for the genome.
(For details see, the wiki documentation on IGB Quickload.) Modify this so that a user can specific the genome file using the "file" tag. e.g., {code} <file name="foo.2bit" reference="true"/> {code} and {code} <file name="https://example.com/foo.2bit" reference="True"/> {code} and {code} <file name="http://example.com/foo.2bit" reference="True"/> {code} For example 2bit files corresponding to various genomes, see: * http://hgdownload.soe.ucsc.edu/goldenPath This location contains multiple subdirectories for different genome versions. For example, * http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/ contains a file named mm10.2bit (http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/mm10.2bit) which contains the same data shown for IGB genome version M_musculus_Dec_2011. |
| Attachment | SARS-genome.png [ 14885 ] |
| Attachment | quickload.tar.gz [ 14886 ] |
| Attachment | SARS-genome.png [ 14887 ] |
| Attachment | SARS-genome.png [ 14885 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Sprint | Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct [ 103, 104 ] | Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23 [ 103, 104, 106 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Assignee | Chirag Chandrahas Shetty [ chirag24 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Chirag Chandrahas Shetty [ chirag24 ] | Noor Zahara [ noor91zahara ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Assignee | Noor Zahara [ noor91zahara ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Assignee | Chester Dias [ cdias1 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Chester Dias [ cdias1 ] | Noor Zahara [ noor91zahara ] |
| Link | This issue relates to IGBF-337 [ IGBF-337 ] |
| Fix Version/s | 9.1.6 Major Release [ 10604 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Assignee | Noor Zahara [ noor91zahara ] | Nowlan Freese [ nfreese ] |
| Sprint | Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23 [ 103, 104, 106 ] | Fall 1: 14 Sep - 25 Sep, Fall 2: 28 Sep - 9 Oct, Fall 3: Oct 12 - Oct 23, Fall 6 Nov 30 - Dec 11 [ 103, 104, 106, 109 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Nowlan Freese [ nfreese ] | Ann Loraine [ aloraine ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] | Nowlan Freese [ nfreese ] |
| Assignee | Nowlan Freese [ nfreese ] | Noor Zahara [ noor91zahara ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Resolution | Done [ 10000 ] | |
| Status | Closed [ 6 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |