wurmlab/

sequenceserver

Intuitive local web frontend for the BLAST bioinformatics tool

Owners:

$0.00

USD raised

Recent activities

yeban added the repository

over 5 years ago

Issues

Funded Unfunded Rewarded Closed

Command Line Options does not work: cannot load such file -- sequenceserver

Unfunded#589created bylesser-panda

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Long seqids should be truncated in the sidebar

Unfunded#570created byyeban

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large query doesn't respect UI boundaries

Unfunded#571created byMatthAlex

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Running blast on sequenceserver is very slow

Unfunded#573created bynaity2

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Multiple directories

Unfunded#575created bymarcadella

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job.yaml should include more info

Unfunded#576created byyannickwurm

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Run sequenceserver on a RHEL server

Unfunded#577created bynaity2

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Where are BLAST results stored?

Unfunded#578created bynaity2

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Is it possible to skip capybara tests if geckodriver is not installed?

Unfunded#584created byyeban

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ruby versions - need to migrate support

Unfunded#585created byyannickwurm

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refactor exec call to avoid running shell on user provided parameters

Unfunded#569created byrobertvi

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inappropriate text wrapping in header of HSPs

Unfunded#593created byyannickwurm

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Errors in browser in browser console after ES6 migration

Unfunded#602created byyeban

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Some options aren't listed

Unfunded#608created byyannickwurm

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Readme wants to indicate how to run jest tests

Unfunded#615created byyannickwurm

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sequenceserver -m, -l, -s, etc. break on blastdbcmd call

Unfunded#617created bysammyjava

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Sharetocloud

Unfunded#622created byyannickwurm

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System error: BLAST failed abruptly (exit status: 135). Most likely there is a problem with the BLAST+ binaries.

Unfunded#623created byyondchang

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System error in blast

Unfunded#624created byuauy

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Error msg when trying to download the hits FASTA files

Unfunded#625created byypoh1

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react is outdated

Unfunded#556created byyannickwurm

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seqid is modified for some databases

Unfunded#536created byloraine-gueguen

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Selecting bug in rc8

Unfunded#537created byyannickwurm

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update url in About section

Unfunded#543created bydiscoform

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Edit search - rc8

Unfunded#544created byyannickwurm

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(SequenceServer::DATABASE_DIR_NOT_SET)

Unfunded#546created byimane-boudell

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SequenceServer will not download fasta files

Unfunded#547created byleogg-github

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** Could not bind to port 4567.

Unfunded#548created byleogg-github

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If no hits, FASTA and alignment download buttons should be deactivated

Unfunded#552created byyannickwurm

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website

Unfunded#553created byyannickwurm

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BLAST failed abruptly (exit status: 3)

Unfunded#628created byindirasb

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seqserv reports v5 multipart databases as incompatible and prompts user to reformat them

Unfunded#557created byyeban

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If 1 query and 0 hits, I cannot edit my search

Unfunded#558created byyannickwurm

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Rework database compatibility detection

Unfunded#559created byyannickwurm

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"select all" gets stuck to state if "Nucleotide databases" are manually selected first and the "select all" is subsequently used.

Unfunded#562created byMatthAlex

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NCBI has been shifting to using gene identifiers that have greater numbersthan what BLAST has supported

Unfunded#563created byyannickwurm

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footer should be 1 line and not include twitter

Unfunded#564created byyannickwurm

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Blast by similarity failed.

Unfunded#566created byAkifb123

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Add "share" link on the left under downloads

Unfunded#568created byyannickwurm

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exporting large numbers of hit sequences creates too long a command-line

Unfunded#751created byyannickwurm

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Improve labels of titles in result page

Unfunded#698created byyannickwurm

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version bump -> NCBI 2.2.15

Unfunded#703created byyannickwurm

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installation problems on Ubuntu 23.10

Unfunded#706created bythekswenson

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NoMethodError for SequenceServer.makeblastdb.any_to_format?

Unfunded#707created bythekswenson

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Sidebar Element Click Causes Exception and User Work Loss

Unfunded#712created bygorsyan

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Remember user defaults

Unfunded#715created byyannickwurm

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Use params from last search

Unfunded#16created byyeban

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genome fastas beginning with Ns aren't correctly identified

Unfunded#727created byyannickwurm

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When exporting "Kablammo" plot as SVG or PNG, would be useful to have the query index & name appended

Unfunded#736created byphotocyte

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"Advanced parameters:" label in search interface should not be a hyperlink

Unfunded#695created byyannickwurm

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New/Clean install doesn't work

Unfunded#755created bywolfgangrumpf

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New install crashing if blast is not installed

Unfunded#761created bytadast

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blast/task.rb does not find blast binaries

Unfunded#781created bykuntzagk

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BLAST button not working with sequenceserver 3.1.3 and tree widget enabled

Unfunded#784created bylukaszsobala

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don't unfold the first 2 graphs

Unfunded#807created byyannickwurm

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Dockerfile node build target Tailwind CSS error

Unfunded#824created bynathanweeks

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Identifier is bottom-aligned while it should be topaligned

Unfunded#826created byyannickwurm

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Cleaning up old files

Unfunded#838created bypelacables

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Job 404 should not throw an exception

Unfunded#666created bytadast

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Why is config.rb invalid after modification?

Unfunded#631created bysoft-lkq

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NoMethodError while running sequenceserver

Unfunded#638created byaevenstad

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Back button leads to frozen submission interface

Unfunded#640created byyannickwurm

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Integrating with JBrowse2

Unfunded#641created byz626093820

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BLAST is not working

Unfunded#642created byAnaPoets

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BLAST is not working

Unfunded#643created byAnaPoets

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Alignment download not necessarily happening

Unfunded#649created byyannickwurm

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Unable to start container with port mapping

Unfunded#652created byjayramr

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Migrate testing from Travis to Github Actions

Unfunded#653created byyannickwurm

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Status updates for long jobs

Unfunded#534created byyannickwurm

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Number of queries stats in job.yaml

Unfunded#669created bytadast

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closed

Unfunded#672created bywangc1106

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docker build for 2.1.0 release fails

Unfunded#673created bynathanweeks

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how to use tree structure of database lists in docker command

Unfunded#674created bywangc1106

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The local sequenceserver can't work with version 2.1.0.

Unfunded#680created byDjangodu

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Update GH actions to use the latest version of BLAST

Unfunded#685created bytadast

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Intercept badly formatted FASTA query

Unfunded#691created byyannickwurm

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Protein domains in protein queries

Unfunded#693created byyannickwurm

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Refine assisted setup

Unfunded#135created bywwood

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Ability to change default parameters according to the sequence type/length

Unfunded#394created bysongtaogui

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Forbidden AA not filtered and error not thrown

Unfunded#349created bybordin89

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ubuntu bug large db

Unfunded#341created byyannickwurm

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Can not redirect to original blast page by refreshing the web page

Unfunded#462created byzhangxiang36

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2.0 and legacy database format

Unfunded#463created byenuggetry

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How do you define a proxy path/route in Apache

Unfunded#464created byenuggetry

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Database not found if the name ends with 2 digits or more, in release 1.0.13

Unfunded#465created byloraine-gueguen

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Ability to optionally open results in a new tab

Unfunded#467created byyeban

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running sequenceserver in docker- echo status and disable questions

Unfunded#468created bymjy

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postmessage height to cross domain iframe

Unfunded#395created bysongtaogui

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rc3 installation issue - can't make blast dbs (SequenceServer::CommandFailed)

Unfunded#469created bymjcoynejr

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2.0 Is there an extension API - custom link-outs.

Unfunded#470created byenuggetry

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Error in gem installed seqserver while running clast search over nginx

Unfunded#474created bypeeyushsahu

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document/complete JSON API

Unfunded#250created byaudy

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download FASTA fails

Unfunded#475created byenuggetry

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Docker instance for sequenceserver

Unfunded#476created byenuggetry

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2.0 result directory pruning algorithm

Unfunded#477created byenuggetry

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2.0 is there a way to limit the query sequence size and/or number of sequences

Unfunded#478created byenuggetry

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download taxdb and import xml options

Unfunded#416created byyeban

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Optimise docker image

Unfunded#413created byyeban

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Update BLAST version in Docker image

Unfunded#405created bynathanweeks

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query links not shown if >8 queries

Unfunded#448created bylpoorvin

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Query textbox should be vertically resizable

Unfunded#401created byyeban

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Updated documentation for HPC integration ?

Unfunded#445created byloraine-gueguen

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sequenceserver failed to recognize FASTA files

Unfunded#410created bymictadlo

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New Dockerfile

Unfunded#412created bymictadlo

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Recognise gzipped FASTA files in databases directory

Unfunded#407created byyeban

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blast_formatter issue behind corporate proxy (ncbi-blast-2.10.0+)

Unfunded#458created byBjoernsen

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makeblastdb wrapper should preserve taxonomy id during migration

Unfunded#479created byyeban

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error when enabling soft mask

Unfunded#404created bylpoorvin

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Alignment line breaks are not in the right places

Unfunded#455created byGeneDesign

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Hit length distribution vis is confusing when either query or subject sequences are translated

Unfunded#409created byyeban

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Gem::Ext::BuildError: ERROR: Failed to build gem native extension

Unfunded#403created bya2htray

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Hierarchical display of databases

Unfunded#459created bymichaelbroe

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Problem installing v.2.0

Unfunded#460created bymichaelbroe

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SequenceServer v1.1.0-alpha does not display on older browsers (eg Chrome r42)

Unfunded#333created bysujaikumar

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How would one cache the results?

Unfunded#399created bycghiban

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Idea: database structure/tree

Unfunded#520created byBjoernsen

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View Sequence link raises

Unfunded#511created bymjy

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FASTA Link raises

Unfunded#512created bymjy

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Incompatible database, why?

Unfunded#513created byShellfishgene

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RC8 - Duplicate WORKDIR line in Dockerfile

Unfunded#514created bymjy

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taxid should be optional

Unfunded#515created byyannickwurm

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nucleotide sequence detection fails on file upload [2.0rc8]

Unfunded#516created byyannickwurm

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help for -task not given [2.0rc8]

Unfunded#517created byyannickwurm

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when too many HSPs, don't namethem all [2.0rc8]

Unfunded#518created byyannickwurm

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Cant get fasta list of hits, sequenceserver 2.0

Unfunded#519created bywpmitchell

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Adding a :require: breaks Docker config?

Unfunded#510created bymjy

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makeblastdb wrapper can overwrite a db with one of its subsets

Unfunded#521created byyeban

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Probably can't provide multiple -taxids through advanced params input

Unfunded#522created byyeban

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stats, analytics, history

Unfunded#524created byenuggetry

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UX: Delay when clicking "BLAST" when large upload/slow internet

Unfunded#526created byyannickwurm

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Input sequence by url

Unfunded#528created byprometheusloong

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Improved Display of a Long List of Database

Unfunded#307created bynathanhaigh

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whichdb() method causes error when blasting versus multiple DB

Unfunded#529created byjvera888

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systemctl error

Unfunded#533created byprometheusloong

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Upper query field not available after a blast search

Unfunded#492created byTom-A-MD

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makeblastdb wrapper should be always run on startup

Unfunded#480created byyeban

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Clear sessionStorage on unload in search.js

Unfunded#481created byyeban

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Could not run 2.0.0.rc6 without internet connection

Unfunded#482created byvks4git

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Capybara test suite for funky_ids database

Unfunded#483created byyeban

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Fix Travis

Unfunded#484created byyeban

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Automatic multi-part database creation

Unfunded#392created byyeban

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Improve FASTA Download

Unfunded#485created byenuggetry

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Pre-fill sequence textarea on default page with POST (without databases[] or advanced)

Unfunded#491created bysammyjava

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sequenceserver --doctor improvements

Unfunded#320created byyeban

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Config file not found is written too often

Unfunded#457created byyannickwurm

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SequenceServer image size

Unfunded#495created bynathanweeks

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Docker imge build error using BuildKit

Unfunded#502created bynathanweeks

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Browser "back" button function

Unfunded#386created bytomas-pluskal

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link to Apollo

Unfunded#505created bymictadlo

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Wrong identity values in summary

Unfunded#506created byEtienneBucher

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sort databases in categories

Unfunded#507created bydsmlab

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rc8 conversion "No sequences matched any of the taxids provided"

Unfunded#508created bymjy

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Sequence server takes exceedingly long time to echo ready in docker-compose environment

Unfunded#509created bymjy

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Recent activities

yeban added the repository

over 5 years ago

sequenceserver

$0.00

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