-
+
- + Changelog +
-
@@ -124,13 +129,13 @@
- +@@ -140,53 +145,89 @@
NCBI - BioSample
- Source:vignettes/biosample_submission.Rmd+ Source:vignettes/biosample_submission.Rmdbiosample_submission.RmdNCBI - BioSample
---Overview
-BioSample is a database containing aggregated information pertaining to reference samples and samples stored in the European Bioinformatics Institute assay databases.
-Before one can upload experimental samples to BioSample database using
+seqsender, they must ensure the requirement files (such asconfig.yaml,metadata.csv,sequence.fasta,raw reads, etc.) are prepared ahead of time and stored in a submission directory of choice.+-Overview +
+BioSample is a database containing aggregated +information pertaining to reference samples and samples stored in the European Bioinformatics Institute +assay databases.
+Before submitters can upload their experimental samples to +BioSample database using
seqsender, they +must ensure the requirement files (such asconfig.yaml, +metadata.csv,sequence.fasta, +raw reads, etc.) are already prepared ahead of time and +stored them in a submission folder of choice (e.g., +submission_name) within a parent submission directory +(e.g.,submission_dir). That wayseqsender+will be able to scoop up the necessary files in that folder, generate +submission files, and then batch uploading them to the submitting +database of choices.--Requirement files
++-Requirement files +
-
-Config file in a
yamlformat
+Config file in a -
-Metadata file in a
csvformat
+Metadata file in a
yaml+formatcsv+format--Config file
-Config file is a yaml file that provides a brief description about the submission and contains user credentials that allow
+seqsenderto authenticate the database prior to upload a submission.A quick look of where to store all of the requirement files
+
+
+-Config file +
+Config file is a yaml file that provides a brief description about +the submission and contains user credentials that allow +
seqsenderto authenticate the database prior to upload a +submission.
-` NOTE:
++NOTE:
-
-
- To submit to NCBI only, one can remove the GISAID Submission (b) section from the config file. Vice versa, to submit to GISAID only, just remove the NCBI Submission (a) section.
+ - To submit to NCBI only, one can remove the GISAID Submission
+(b) section from the config file. Vice versa, to submit to
+GISAID only, just remove the NCBI Submission (a)
+section.
-
-Submission_Position determines the order of databases in which we will submit to first. For instance, if GISAID is set as
Primary, seqsender will submit to GISAID first, then after all samples are assigned with a GISAID accession number, seqsender will proceed to submit to NCBI. This order of submission ensures samples are linked correctly between the two databases.
+Submission_Position determines the order of +databases in which we will submit to first. For instance, if GISAID is +set as1, seqsender will submit +to GISAID first, then after all samples are assigned with a GISAID +accession number, seqsender will proceed to +submit to NCBI. This order of submission ensures samples are linked +correctly between the two databases.
- -Username and Password under the NCBI Submission (b) section are the credentials used to authenticate the NCBI FTP Server (not to mistake with individual NCBI account). See PRE-REQUISITES for more details. +Username and Password under the +NCBI Submission (b) section are the credentials used to +authenticate the NCBI FTP Server (not to mistake with +individual NCBI account). See PRE-REQUISITES +for more details.
--Metadata file
-Here is a short description about the fields in the metadata worksheet.
++@@ -345,11 +421,13 @@Metadata file +
+The metadata worksheet is a comma-delimited (csv) file that contains +required attributes that are useful for the rapid analysis and trace +back of Influenza A Virus or SARS-COV-2 cases.
+Here is a short description about the fields in the metadata +worksheet.
@@ -202,7 +243,8 @@ sequence_name
-Sequence identifier used in fasta file. This is used to create the fasta file for Genbank or GISAID. +Sequence identifier used in fasta file. This is used to create the fasta +file for Genbank or GISAID. @@ -210,7 +252,12 @@ organism
-The most descriptive organism name for the samples. If relevant, you can search the organism name in the NCBI Taxonomy database. For FLU, organism must be “Influenza A Virus”. For COV, organism must be “Severe acute respiratory syndrome coronavirus 2”. +The most descriptive organism name for the samples. If relevant, you can +search the organism name in the +NCBI +Taxonomy database. For FLU, organism must be “Influenza A +Virus”. For COV, organism must be “Severe acute respiratory +syndrome coronavirus 2”. @@ -218,7 +265,8 @@ collection_date
-The date on which the sample was collected; must be in the ISO format: YYYY-MM-DD.
For example: 2020-03-25 +The date on which the sample was collected; must be in the ISO format: +YYYY-MM-DD.
For example: 2020-03-25@@ -226,7 +274,9 @@ authors
-Citing authors. List of Last, First Middle, suffix separated by a semicolon “;” E.g.: “Baker, Howard Henry, Jr.; Powell, Earl Alexander, III.;” +Citing authors. List of Last, First Middle, suffix separated by a +semicolon “;” E.g.: “Baker, Howard Henry, Jr.; Powell, Earl Alexander, +III.;” @@ -234,7 +284,9 @@ ncbi-spuid
-Submitter Provided Unique Identifiers. This is used to report back assigned accessions as well as for cross-linking objects within submission. +Submitter Provided Unique Identifiers. This is used to report back +assigned accessions as well as for cross-linking objects within +submission. @@ -242,7 +294,9 @@ ncbi-spuid_namespace
-If SPUID is used, spuid_namespace has to be provided. The values of spuid_namespace are from controlled vocabulary and need to be coordinated with NCBI prior to submission. +If SPUID is used, spuid_namespace has to be provided. The values of +spuid_namespace are from controlled vocabulary and need to be +coordinated with NCBI prior to submission. @@ -258,7 +312,8 @@ bs-description
-A brief description about the sample, e.g. SARS-CoV-2 Sequencing Baseline Constellation. +A brief description about the sample, e.g. SARS-CoV-2 Sequencing +Baseline Constellation. @@ -274,7 +329,12 @@ bs-geo_loc_name
-Geographical origin of the sample; use the appropriate name from this list. Use a colon to separate the country or ocean from more detailed information about the location, eg “Canada: Vancouver” or “Germany: halfway down Zugspitze, Alps”. Entering multiple localities in one attribute is not allowed. +Geographical origin of the sample; use the appropriate name from +this +list. Use a colon to separate the country or ocean from more +detailed information about the location, eg “Canada: Vancouver” or +“Germany: halfway down Zugspitze, Alps”. Entering multiple localities in +one attribute is not allowed. @@ -282,7 +342,8 @@ bs-host
-The natural (as opposed to laboratory) host to the organism from which the sample was obtained. Use the full taxonomic name, eg, Homo sapiens. +The natural (as opposed to laboratory) host to the organism from which +the sample was obtained. Use the full taxonomic name, eg, Homo sapiens. @@ -290,7 +351,11 @@ bs-host_disease
-Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled vocabulary, please see Human Disease Ontology or MeSH +Name of relevant disease, e.g. Salmonella gastroenteritis. Controlled +vocabulary, please see +Human +Disease Ontology or +MeSH @@ -298,7 +363,8 @@ bs-isolate
-Identification or description of the specific individual from which this sample was obtained. +Identification or description of the specific individual from which this +sample was obtained. @@ -306,7 +372,8 @@ bs-isolation_source
-Describes the physical, environmental and/or local geographical source of the biological sample from which the sample was derived. +Describes the physical, environmental and/or local geographical source +of the biological sample from which the sample was derived. @@ -314,21 +381,30 @@ bs-lat_lon
-The geographical coordinates of the location where the sample was collected. Specify as degrees latitude and longitude in format “d[d.dddd] N|S d[dd.dddd] W|E”, eg, 38.98 N 77.11 W +The geographical coordinates of the location where the sample was +collected. Specify as degrees latitude and longitude in format +“d[d.dddd] N|S d[dd.dddd] W|E”, eg, 38.98 N 77.11 W
-NOTE: The prefix of “bs-” is used to identity attributes for BioSample submissions
-To include additional attributes to BioSample submissions, just append
+bs-in front of the desired attributes, e.g.bs-host_age, bs-host_sex, etc. See Pathogen.cl.1.0 package for more attributes.NOTE: The prefix of “bs-” is used +to identity attributes for BioSample submissions
+To include additional attributes to BioSample +submissions, just append
bs-in front of the desired +attributes, e.g.bs-host_age, bs-host_sex, etc. See Pathogen.cl.1.0 +package for more attributes.
--- You are now ready to install
+seqsenderand batch upload your submission -+ +You are now ready to install
seqsenderand batch upload +your submission +
-Any questions or issues? Please report them on our Github issue tracker.
+Any questions or issues? Please report them on our +Github +issue tracker.
@@ -358,5 +436,7 @@
+ + diff --git a/docs/articles/compose_installation.html b/docs/articles/compose_installation.html index cfb2d1d..2b7a522 100644 --- a/docs/articles/compose_installation.html +++ b/docs/articles/compose_installation.html @@ -19,6 +19,8 @@ + +
@@ -31,7 +33,7 @@@@ -44,7 +46,7 @@- - + Getting Started @@ -69,7 +71,7 @@
- - + Databases @@ -95,7 +97,7 @@
- - + Support @@ -108,6 +110,9 @@
-
+
- + Changelog +
-
@@ -124,13 +129,13 @@
- +@@ -157,281 +162,407 @@
How to run seqsender with Compose
- Source:vignettes/compose_installation.Rmd+ Source:vignettes/compose_installation.Rmdcompose_installation.RmdHow to run seqsender with Compose
- Standard utilities: curl, tar, unzip
ADDITIONAL REQUIREMENTS:
-See PRE-REQUISITES and REQUIREMENT FILES before proceeding to the next steps
---(1) Clone
- +seqsenderrepo to your $HOME directorySee PRE-REQUISITES +and REQUIREMENT +FILES before proceeding to the next steps
+ ---(2) Navigate to
seqsenderfolder wheredocker-compose.ymlis stored and edit that file to link the data inputs to runseqsender++-(2) Navigate to
- -seqsenderfolder where +docker-compose.ymlis stored and edit that file to link the +data inputs to runseqsenderHere is a quick look of the
-docker-compose.yamlfile:
-version: "3.9" - -x-data-volumes: - &data-volume - type: bind - source: $HOME - target: /data - -services: - seqsender: - container_name: seqsender - image: cdcgov/seqsender-dev:latest - restart: always - volumes: - - *data-volume - command: tail -f /dev/nullNOTE:
+ +sourceis the storage location of your local machine. This location will be mapped to/datadirectory inside the container. Here we are mounting the local$HOMEdirectory to/datainside the container.Here is a quick look of the
+docker-compose.yaml+file:+version: "3.9" + +x-data-volumes: + &data-volume + type: bind + source: $HOME + target: /data + +services: + seqsender: + container_name: seqsender + image: cdcgov/seqsender-dev:latest + restart: always + volumes: + - *data-volume + command: tail -f /dev/nullNOTE:
sourceis the storage +location of your local machine. This location will be mapped to +/datadirectory inside the container. Here we are mounting +the local$HOMEdirectory to/datainside the +container.--(3) Start up the
- -seqsendercontainer
--d: run the container in detached modeFor more information about the docker-compose syntax, see docker-compose up reference
++-(3) Start up the
+ +seqsendercontainer +
+-d: run the container in detached mode +For more information about the docker-compose syntax, see +docker-compose +up reference
--(4) Check if the container is running
-+ -docker container ps - - -CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES -b37b6b19c4e8 seqsender:latest "/bin/bash" 5 hours ago Up 5 hours seqsender--(5) See a list of commands in
- -seqsendercontainer
--t: allocate a pseudo-tty
-i: keep STDIN open even if not attached-h,--help: show help messages and exit-usage: seqsender.py [-h] - {prep,submit,check_submission_status,template,version} ... - -Automate the process of batch uploading consensus sequences and metadata to -databases of your choices - -positional arguments: - {prep,submit,check_submission_status,template,version} - -optional arguments: - -h, --help show this help message and exitRather than hastily jump in and submit a
+productionsubmission right away, we can utilize GISAID’s and NCBI’s “TEST-SERVER” to upload atestsubmission first. That way submitter can familiarize themselves with the submission process prior to make a real submission.+-(5) See a list of commands in
+ +seqsendercontainer +
+-t: allocate a pseudo-tty
-i: keep STDIN open even if not attached-h,--help: +show help messages and exit+usage: seqsender.py [-h] + {prep,submit,check_submission_status,template,version} ... + +Automate the process of batch uploading consensus sequences and metadata to +databases of your choices + +positional arguments: + {prep,submit,check_submission_status,template,version} + +optional arguments: + -h, --help show this help message and exitRather than hastily jump in and submit a
+production+submission right away, we can utilize GISAID’s and NCBI’s +“TEST-SERVER” to upload atestsubmission +first. That way submitter can familiarize themselves with the submission +process prior to make a real submission.Note: Duplicate test submissions will result in an +error. Please create new sequence names each time you plan to run test +submissions to avoid this issue.
-- Submit a
testsubmission with a pre-processed dataset ++@@ -625,11 +841,13 @@+ +Submit a
- +testsubmission with a pre-processed +dataset++ +Submit a
testsubmission with your own dataset
-Any questions or issues? Please report them on our Github issue tracker.
+Any questions or issues? Please report them on our +Github +issue tracker.
3. Check the status of a submission< @@ -638,5 +856,7 @@
3. Check the status of a submission< + +
-
-Config file in a
