diff --git a/_sources/vobs/vobs-data-access.ipynb b/_sources/vobs/vobs-data-access.ipynb index ff46a15..a7f1d91 100644 --- a/_sources/vobs/vobs-data-access.ipynb +++ b/_sources/vobs/vobs-data-access.ipynb @@ -17,35 +17,39 @@ "\n", "To access data from the Vector Observatory, you will need to follow these steps:\n", "\n", - "### Step 1. Make sure you have a Google Account\n", + "#### Step 1. Make sure you have a Google Account\n", "\n", "To allow us to configure data access permissions, you will need to provide us with an email address that is associated with a Google account. This could be a standard Google (i.e., GMail) account, or alternatively it could be your work email if your employer uses Google Workspace.\n", "\n", - "### Step 2. Fill out the data access request form\n", + "#### Step 2. Fill out the data access request form\n", "\n", "Please fill out and submit the following form:\n", "\n", - "https://forms.gle/kCqistorZyxaU4LP7 \n", + "> [MalariaGEN cloud data access form](https://forms.gle/kCqistorZyxaU4LP7)\n", "\n", "All requests for data access will be granted, subject to verification checks and agreement to reasonable use. This is to ensure that the data resources remain accessible to everyone. Submitting this form will allow us to configure storage permissions and monitor storage for excessive network usage in future.\n", "\n", - "### Step 3. Ensure you are using the latest version of the `malariagen_data` Python package\n", + "#### Step 3. Ensure you are using the latest version of the `malariagen_data` Python package\n", "\n", "If you access data via the `malariagen_data` Python package, please upgrade to version 9.0 or higher. These versions will automatically use your authentication credentials when accessing data in Google Cloud.\n", "\n", - "### Step 4. Set up Google Cloud authentication credentials\n", + "#### Step 4. Set up Google Cloud authentication credentials\n", "\n", - "If you are only accessing data via the malariagen_data Python package from within Google Colab, you can skip this step, because authentication credentials will be obtained automatically.\n", + "If you are only accessing data via the `malariagen_data` Python package from within Google Colab, you can skip this step, because authentication credentials will be obtained automatically.\n", "\n", "If you are accessing data from any other location, you will need to authenticate with Google Cloud. To do this, you will need to:\n", "\n", "1. Install the [Google Cloud CLI](https://cloud.google.com/sdk/gcloud). See the details in the Google Documentation [here](https://cloud.google.com/sdk/docs/install-sdk).\n", "\n", - "2. Check gcloud is installed correctly:\n", + "\n", + "2. Check `gcloud` is installed correctly:\n", "\n", "```bash\n", "gcloud help\n", "```\n", + "\n", + "3. Authenticate using `gcloud`: \n", + "\n", "- If you need to authenticate within the `malariagen_data` package, you will need to use the following command:\n", "\n", "```bash\n", @@ -56,18 +60,16 @@ "\n", "```bash\n", "gcloud auth login\n", - "```\n", - "\n", - "If you have any questions, please contact us at: support@malariagen.net" + "```" ] }, { - "cell_type": "code", - "execution_count": null, - "id": "ade225aa-7bd3-44e6-95a6-17e81cb53557", + "cell_type": "markdown", + "id": "ed024cac-be61-44a0-a339-821a9f70a456", "metadata": {}, - "outputs": [], - "source": [] + "source": [ + "If you have any questions, please contact us at: " + ] } ], "metadata": { diff --git a/searchindex.js b/searchindex.js index 8a2550a..03f30e7 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ 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(Ag1000G phase 3)","Ag3.1","Ag3.2","Ag3.3","Ag3.4","Ag3.5","Ag3.6","Ag3.7","Ag3.8","Ag3.9","Ag3 analysis","Ag3 API","Ag3 cloud data access","Ag3 data downloads","Ag3 sequencing and variant calling methods","Amin1 API","Amin1.0 cloud data access","Amin1.0 data downloads","Amin1.0","MalariaGEN vector data user guide","Release notes","Ag1000G partner studies","Vector Observatory Data Access"],titleterms:{"0":[0,16,17,18],"02":20,"03":20,"04":20,"07":20,"09":20,"1":[1,21,22],"11":20,"12":20,"14":20,"15":20,"2":[2,21,22],"2021":20,"2022":20,"3":[0,3,21,22],"4":[4,22],"5":5,"6":6,"7":7,"8":8,"9":9,"c\u00f4te":21,"public":21,The:21,access:[12,16,22],account:22,acknowledg:[14,21],african:21,ag1000g:[0,21],ag3:[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14],aim:14,align:[13,14,17],all:14,allel:[12,13,14,16],amin1:[15,16,17,18],an:14,analys:14,analysi:10,ancestri:14,angola:21,anomali:14,anophel:19,api:[11,15],appendic:14,ar:22,arabiensi:14,assign:14,authent:22,bam:[13,17],bioko:21,bissau:21,burkina:21,calcul:14,call:[0,1,2,3,4,5,6,7,8,9,12,13,14,16,17,18],cameroon:21,central:21,citat:18,cloud:[12,16,22],cnv:[12,13,14],collect:13,coloni:[14,21],coluzzii:14,commun:19,complex:19,comput:[12,16],congo:21,contamin:14,contributor:21,copi:[12,13,14],count:16,coverag:[12,13,14],credenti:22,cross:[14,21],d:21,data:[0,1,2,3,4,5,6,7,8,9,12,13,16,17,18,19,22],democrat:21,detect:14,discord:[12,13,14],discoveri:14,download:[13,17],ensur:22,exampl:[12,16],faso:21,fastq:13,feedback:[12,13,16,17],fill:22,filter:[12,13,14,16],form:22,format:[13,17],further:[0,1,2,3,4,5,6,7,8,9,18],gabon:21,gambia:[14,19,21],genom:[0,1,2,3,4,5,6,7,8,9,14,16,18,19],genotyp:[12,13,16],ghana:21,googl:22,guid:19,guinea:21,haplotyp:[12,13,14],have:22,hmm:[12,13,14],host:[0,1,2,3,4,5,6,7,8,9,12,13,16,17,18],identifi:14,infer:14,inform:[14,21],input:14,insecticid:14,island:21,ivoir:21,joint:14,kenya:21,larger:12,latest:22,loci:14,make:22,malaria:19,malariagen:19,malariagen_data:22,malawi:21,mali:21,marker:14,mayott:21,metadata:[12,13,16,17],method:14,minimu:19,model:14,mozambiqu:21,normal:14,note:[19,20],number:[12,13,14],observatori:[19,22],out:22,outlier:14,packag:22,panel:13,partner:[0,1,2,3,4,5,6,7,8,9,14,18,19,21],pass:16,pca:14,phase:[0,14],popul:[0,14,18],posit:16,python:22,qc:14,raw:13,read:[0,1,2,3,4,5,6,7,8,9,12,13,14,17,18],refer:[13,16,21],releas:[19,20],replic:14,republ:21,request:22,resist:14,resourc:21,run:12,sampl:[0,1,2,3,4,5,6,7,8,9,12,13,14,16,17,18,21],segreg:16,sequenc:[0,1,2,3,4,5,6,7,8,9,13,14,17,18],set:[0,1,2,3,4,5,6,7,8,9,12,13,21,22],setup:[12,16],sex:14,site:[12,13,14,16],snp:[12,13,14,16,17],speci:[13,14],specimen:13,state:14,statist:14,step:22,studi:[0,1,2,3,4,5,6,7,8,9,14,18,21],subset:12,suggest:[12,13,16,17],summari:14,sure:22,tanzania:21,technic:14,term:[0,1,2,3,4,5,6,7,8,9,18],three:14,uganda:21,up:22,us:[0,1,2,3,4,5,6,7,8,9,12,14,18,22],user:19,variant:[0,1,2,3,4,5,6,7,8,9,14,18],variat:[12,13],vcf:[13,17],vector:[19,22],version:22,via:14,whole:[0,1,2,3,4,5,6,7,8,9,14,18],wide:14,you:22,zarr:13}}) \ No newline at end of file diff --git a/vobs/vobs-data-access.html b/vobs/vobs-data-access.html index 7d80661..b5a0e90 100644 --- a/vobs/vobs-data-access.html +++ b/vobs/vobs-data-access.html @@ -618,7 +618,9 @@

Step 1. Make sure you have a Google Account

Step 2. Fill out the data access request form#

Please fill out and submit the following form:

-

https://forms.gle/kCqistorZyxaU4LP7

+
+

MalariaGEN cloud data access form

+

All requests for data access will be granted, subject to verification checks and agreement to reasonable use. This is to ensure that the data resources remain accessible to everyone. Submitting this form will allow us to configure storage permissions and monitor storage for excessive network usage in future.

@@ -627,15 +629,18 @@

Step 3. Ensure you are using the latest version of the

Step 4. Set up Google Cloud authentication credentials#

-

If you are only accessing data via the malariagen_data Python package from within Google Colab, you can skip this step, because authentication credentials will be obtained automatically.

+

If you are only accessing data via the malariagen_data Python package from within Google Colab, you can skip this step, because authentication credentials will be obtained automatically.

If you are accessing data from any other location, you will need to authenticate with Google Cloud. To do this, you will need to:

  1. Install the Google Cloud CLI. See the details in the Google Documentation here.

    2. -

  2. Check gcloud is installed correctly:

    3. +

  3. Check gcloud is installed correctly:

gcloud help
+
    +

  1. Authenticate using gcloud:

    2. +

  • If you need to authenticate within the malariagen_data package, you will need to use the following command:

@@ -648,7 +653,7 @@

Step 4. Set up Google Cloud authentication credentials
gcloud auth login
-

If you have any questions, please contact us at: support@malariagen.net

+

If you have any questions, please contact us at: mailto:support@malariagen.net