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Update the downloading links for biominer-aget.
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yjcyxky committed Oct 9, 2024
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34 changes: 17 additions & 17 deletions docs/getting_started/request_omics_data.md
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Expand Up @@ -21,76 +21,76 @@ More details on the data policies can be found in [the document](../policies/dat

### 3. How to bulk download the omics data files with file transfer tool?

- Download a metadata table from multi-omics data page.(such as genomics data in <a href="https://www.chinese-quartet.org/#/data/download/quartet-genomics" target="_blank">Multiomics Data -> Genomics Data</a>
- Download a metadata table from multi-omics data page.(such as genomics data in <a href="https://www.chinese-quartet.org/#/data/download/quartet-genomics" target="_blank">Multiomics Data -> Genomics Data</a>)

- Get the md5sum of files which you want to download from the metadata table.

- Follow the following docs to download your expected files.

#### 3.1 Download `file transfer tool - biominer-aget`

Click the link to download `BioMiner Aget`:
Click the link to download `BioMiner Aget`:

- [Linux (CentOS, Debian/Ubuntu or Others)](https://www.indexd.org/biominer-aget/biominer-aget_x86-64_linux)
- [Linux (CentOS, Debian/Ubuntu or Others)](https://www.indexd.org/biominer-aget/biominer-aget-x86_64-linux)

- [Mac (Intel, not m1 & m2 version)](https://www.indexd.org/biominer-aget/biominer-aget_x86-64_macosx)
- [Mac (Intel, not m1 & m2 version)](https://www.indexd.org/biominer-aget/biominer-aget-x86_64-mac)

- [Windows](https://www.indexd.org/biominer-aget/biominer-aget_x86-64_windows)
- [Mac ARM64](https://www.indexd.org/biominer-aget/biominer-aget-x86_64-mac-arm64)

- [Windows](https://www.indexd.org/biominer-aget/biominer-aget-x86_64-windows)

Copy the biominer-aget_xxx binary into /usr/bin/biominer-aget_xxx or any other directory which in PATH variable.

!!!note Please note that
1. The `chunk_size` and `concurrency` parameters are related with the download speed. **There may be tens or hundreds of times the difference, so it's worth taking some time to find the best one.**

2. The biominer-aget binary is not available for mac (arm, m1 & m2).

3. Not each file can be found in all these repos, so you need to specify a repo name when you downloading expected file.
2. Not each file can be found in all these repos, so you need to specify a repo name when you downloading expected file.

#### 3.2 Download a data file with biominer-aget
e.g. you want to download the file with UUID `0023a688-6569-44d7-a2cf-b031f4af8cdd` or Hash (such as md5sum, sha128...) `d4e50c8edbf5215fbe2afa1540f7c968` from the repository biominer.fudan-pgx, you can run the following command:

##### For Mac (Intel) Users

```bash
biominer-aget_x86-64_macosx --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000
biominer-aget-x86_64-mac --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000

## or

biominer-aget_x86-64_macosx --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000
biominer-aget-x86_64-mac --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000

## NODE repo doesn't support http range, so the --chunk_size and --concurrency arguments don't work for it.

biominer-aget_x86-64_macosx --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo node
biominer-aget-x86_64-mac --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo node
```

##### For Linux Users

```bash
biominer-aget_x86-64_linux --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000
biominer-aget-x86_64-linux --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000

## or

biominer-aget_x86-64_linux --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000
biominer-aget-x86_64-linux --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo gsa --chunk_size 1m --concurrency 1000

## NODE repo doesn't support http range, so the --chunk_size and --concurrency arguments don't work for it.

biominer-aget_x86-64_linux --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo node
biominer-aget-x86_64-linux --hash d4e50c8edbf5215fbe2afa1540f7c968 --output-dir ~/Downloads/ --repo node
```

##### For Windows Users

If you download the biominer-aget_xxx binary into C://Users/xxx/Desktop, you can use the following command to download data file from QDP.

```cmd
cmd /c C:\Users\xxx\Desktop\biominer-aget_x86-64_windows --hash d4e50c8edbf5215fbe2afa1540f7c968 --repo gsa
cmd /c C:\Users\xxx\Desktop\biominer-aget-x86_64-windows --hash d4e50c8edbf5215fbe2afa1540f7c968 --repo gsa
## or
cmd /c C:\Users\xxx\Desktop\biominer-aget_x86-64_windows --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --repo gsa --chunk_size 1m --concurrency 1000
cmd /c C:\Users\xxx\Desktop\biominer-aget-x86_64-windows --guid biominer.fudan-pgx/0023a688-6569-44d7-a2cf-b031f4af8cdd --repo gsa --chunk_size 1m --concurrency 1000
## NODE repo doesn't support http range, so the --chunk_size and --concurrency arguments don't work for it.
cmd /c C:\Users\xxx\Desktop\biominer-aget_x86-64_windows --hash d4e50c8edbf5215fbe2afa1540f7c968 --repo node
cmd /c C:\Users\xxx\Desktop\biominer-aget-x86_64-windows --hash d4e50c8edbf5215fbe2afa1540f7c968 --repo node
```

```bash
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