From 9bda34eba5657683276b405b6e962bf7f319b66f Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 13:53:51 +0200 Subject: [PATCH 01/23] inital commit of offline usage instructions --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 83fc760..b7da3c6 100644 --- a/README.md +++ b/README.md @@ -62,3 +62,9 @@ Additional parameters to be passed to `metagraph` CLI: - `num_top_labels` (`inf` by default), - `min_kmers_fraction_label` (`0.7` by default), - `min_kmers_fraction_graph` (`0.0` by default). + +### Instructions for offline usage + +## Additional instructions + +For further documentation and usage instructions, please refer to our [Quick start](https://metagraph.ethz.ch/static/docs/quick_start.html) guide in the [MetaGraph documentation](https://metagraph.ethz.ch/static/docs/index.html). The source code is maintained on our [GitHub repository](https://github.com/ratschlab/metagraph). From 2c374ad2636a0d437438c886cc7c496f705320f3 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 16:51:39 +0200 Subject: [PATCH 02/23] update --- README.md | 14 +++++++++++++- 1 file changed, 13 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index fadcd85..0cbdaad 100644 --- a/README.md +++ b/README.md @@ -191,6 +191,18 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ### Instructions for offline usage +MetaGraph can be installed locally for offline use on a Linux or Mac system as follows: +```sh +conda install -c bioconda -c conda-forge metagraph +``` + +Search indexes can be downloaded from (s3://metagraph-data-public)[s3://metagraph-data-public] as follows: +```sh +XYZTODO +``` + +Search queries can then be executing using the same commands as above. + ## Additional instructions -For further documentation and usage instructions, please refer to our [Quick start](https://metagraph.ethz.ch/static/docs/quick_start.html) guide in the [MetaGraph documentation](https://metagraph.ethz.ch/static/docs/index.html). The source code is maintained on our [GitHub repository](https://github.com/ratschlab/metagraph). +For further documentation and usage instructions (including setup instructions using Docker and via source code compilation), please refer to our [Quick start](https://metagraph.ethz.ch/static/docs/quick_start.html) guide in the [MetaGraph documentation](https://metagraph.ethz.ch/static/docs/index.html). The source code is maintained on our [GitHub repository](https://github.com/ratschlab/metagraph). From 28590a98485d6703fc8ba1208155901c6af69363 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 16:54:05 +0200 Subject: [PATCH 03/23] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0cbdaad..8b0a718 100644 --- a/README.md +++ b/README.md @@ -196,7 +196,7 @@ MetaGraph can be installed locally for offline use on a Linux or Mac system as f conda install -c bioconda -c conda-forge metagraph ``` -Search indexes can be downloaded from (s3://metagraph-data-public)[s3://metagraph-data-public] as follows: +Search indexes can be downloaded from [s3://metagraph-data-public](s3://metagraph-data-public) as follows: ```sh XYZTODO ``` From 209435d25376047e865981b814cd394ce83e4c15 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:01:21 +0200 Subject: [PATCH 04/23] Update README.md --- README.md | 29 ++++++++++++++++++++++++----- 1 file changed, 24 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 8b0a718..a014072 100644 --- a/README.md +++ b/README.md @@ -191,17 +191,36 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ### Instructions for offline usage -MetaGraph can be installed locally for offline use on a Linux or Mac system as follows: +MetaGraph can be installed locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public) as follows: ```sh -conda install -c bioconda -c conda-forge metagraph +XYZTODO ``` -Search indexes can be downloaded from [s3://metagraph-data-public](s3://metagraph-data-public) as follows: +#### Conda ```sh -XYZTODO +conda install -c bioconda -c conda-forge metagraph +conda activate metagraph +metagraph query -i graph.primary.small.dbg \ + -a annotation.clean.row_diff_brwt.annodbg \ + --query-mode matches \ + --num-top-labels 10 \ + --min-kmers-fraction-label 0 \ + --min-kmers-fraction-graph 0 \ + 100_studies_short.fq ``` -Search queries can then be executing using the same commands as above. +#### Docker +```sh +docker pull ghcr.io/ratschlab/metagraph:master +docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i graph.primary.small.dbg \ + -a annotation.clean.row_diff_brwt.annodbg \ + --query-mode matches \ + --num-top-labels 10 \ + --min-kmers-fraction-label 0 \ + --min-kmers-fraction-graph 0 \ + 100_studies_short.fq +``` +replacing `${MNTDIR}` with the local mount path. ## Additional instructions From f7a1ac090b69c8968efa500377fb265d65d314ae Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:01:54 +0200 Subject: [PATCH 05/23] Update README.md --- README.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index a014072..54a1ffc 100644 --- a/README.md +++ b/README.md @@ -213,12 +213,12 @@ metagraph query -i graph.primary.small.dbg \ ```sh docker pull ghcr.io/ratschlab/metagraph:master docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i graph.primary.small.dbg \ - -a annotation.clean.row_diff_brwt.annodbg \ - --query-mode matches \ - --num-top-labels 10 \ - --min-kmers-fraction-label 0 \ - --min-kmers-fraction-graph 0 \ - 100_studies_short.fq + -a annotation.clean.row_diff_brwt.annodbg \ + --query-mode matches \ + --num-top-labels 10 \ + --min-kmers-fraction-label 0 \ + --min-kmers-fraction-graph 0 \ + 100_studies_short.fq ``` replacing `${MNTDIR}` with the local mount path. From f361b6b16f910a744df38695b7c08a05ddc60d11 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:08:03 +0200 Subject: [PATCH 06/23] Update README.md --- README.md | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 54a1ffc..7ef02b3 100644 --- a/README.md +++ b/README.md @@ -191,10 +191,11 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ### Instructions for offline usage -MetaGraph can be installed locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public) as follows: +MetaGraph can be installed locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: ```sh -XYZTODO +aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive ``` +Currently, chunks numbered `0001` through to `0400` are available for download. #### Conda ```sh From db5236d23ca457abd84ef89814c5fb0c5545cca1 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:10:38 +0200 Subject: [PATCH 07/23] Update README.md --- README.md | 16 ++++++++++++---- 1 file changed, 12 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 7ef02b3..bbd2dd8 100644 --- a/README.md +++ b/README.md @@ -201,8 +201,12 @@ Currently, chunks numbered `0001` through to `0400` are available for download. ```sh conda install -c bioconda -c conda-forge metagraph conda activate metagraph -metagraph query -i graph.primary.small.dbg \ - -a annotation.clean.row_diff_brwt.annodbg \ +``` + +Followed by a query on chunk `0001` using the command +```sh +metagraph query -i 0001/graph.primary.small.dbg \ + -a 0001/annotation.clean.row_diff_brwt.annodbg \ --query-mode matches \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ @@ -213,8 +217,12 @@ metagraph query -i graph.primary.small.dbg \ #### Docker ```sh docker pull ghcr.io/ratschlab/metagraph:master -docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i graph.primary.small.dbg \ - -a annotation.clean.row_diff_brwt.annodbg \ +``` + +Followed by a query on chunk `0001` using the command +```sh +docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0001/graph.primary.small.dbg \ + -a 0001/annotation.clean.row_diff_brwt.annodbg \ --query-mode matches \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ From 41337fe9e73eaea982d53ed58e25f1904472682b Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:16:26 +0200 Subject: [PATCH 08/23] Update README.md --- README.md | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index bbd2dd8..df35e80 100644 --- a/README.md +++ b/README.md @@ -195,7 +195,10 @@ MetaGraph can be installed locally for offline use on a Linux or a Mac host usin ```sh aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive ``` -Currently, chunks numbered `0001` through to `0400` are available for download. +Currently, chunks numbered `0001` through to `0400` are available for download. The example query file can be downloaded as follows: +```sh +aws s3 cp examples/100_studies_short.fq . +``` #### Conda ```sh From eeab3ef211cedbe7917b84cdbfcd175b3779ccba Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:22:18 +0200 Subject: [PATCH 09/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index df35e80..d498b31 100644 --- a/README.md +++ b/README.md @@ -189,7 +189,7 @@ metagraph query -i graph.primary.small.dbg \ Then, it will save the resulting file in the S3. When all chunks are processed, a dedicated script will merge the results in a single file and send you a notification. -### Instructions for offline usage +## Instructions for offline usage MetaGraph can be installed locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: ```sh From 6028d8e6c92c0e0849c0daa960e79078b2dd411e Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:22:36 +0200 Subject: [PATCH 10/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index d498b31..ae765e6 100644 --- a/README.md +++ b/README.md @@ -191,7 +191,7 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ## Instructions for offline usage -MetaGraph can be installed locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: +MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: ```sh aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive ``` From 198f705ede3e2e347bfa5b9bf9aa8a377411983e Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:24:49 +0200 Subject: [PATCH 11/23] Update README.md --- README.md | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/README.md b/README.md index ae765e6..5b2dd67 100644 --- a/README.md +++ b/README.md @@ -195,10 +195,7 @@ MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) loc ```sh aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive ``` -Currently, chunks numbered `0001` through to `0400` are available for download. The example query file can be downloaded as follows: -```sh -aws s3 cp examples/100_studies_short.fq . -``` +Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under `examples/100_studies_short.fq`. #### Conda ```sh @@ -214,7 +211,7 @@ metagraph query -i 0001/graph.primary.small.dbg \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ --min-kmers-fraction-graph 0 \ - 100_studies_short.fq + examples/100_studies_short.fq ``` #### Docker @@ -230,7 +227,7 @@ docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0001/gr --num-top-labels 10 \ --min-kmers-fraction-label 0 \ --min-kmers-fraction-graph 0 \ - 100_studies_short.fq + examples/100_studies_short.fq ``` replacing `${MNTDIR}` with the local mount path. From 2cae7b55352866dbee227a3cfc0a8480dce9f986 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:27:17 +0200 Subject: [PATCH 12/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 5b2dd67..565b62a 100644 --- a/README.md +++ b/README.md @@ -193,7 +193,7 @@ Then, it will save the resulting file in the S3. When all chunks are processed, MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: ```sh -aws s3 cp metagraph-data-public/all_sra/data/metagenome/0001 . --recursive +aws s3 cp s3://metagraph-data-public/all_sra/data/metagenome/0001 . --recursive ``` Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under `examples/100_studies_short.fq`. From 74224f3525c4e87e4f6f9f9e8c7e20a06deea2ae Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:28:16 +0200 Subject: [PATCH 13/23] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 565b62a..637cb69 100644 --- a/README.md +++ b/README.md @@ -191,9 +191,9 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ## Instructions for offline usage -MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0001` can be downloaded to a working directory as follows: +MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows: ```sh -aws s3 cp s3://metagraph-data-public/all_sra/data/metagenome/0001 . --recursive +aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --recursive ``` Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under `examples/100_studies_short.fq`. @@ -203,10 +203,10 @@ conda install -c bioconda -c conda-forge metagraph conda activate metagraph ``` -Followed by a query on chunk `0001` using the command +Followed by a query on chunk `0400` using the command ```sh -metagraph query -i 0001/graph.primary.small.dbg \ - -a 0001/annotation.clean.row_diff_brwt.annodbg \ +metagraph query -i 0400/graph.primary.small.dbg \ + -a 0400/annotation.clean.row_diff_brwt.annodbg \ --query-mode matches \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ @@ -221,8 +221,8 @@ docker pull ghcr.io/ratschlab/metagraph:master Followed by a query on chunk `0001` using the command ```sh -docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0001/graph.primary.small.dbg \ - -a 0001/annotation.clean.row_diff_brwt.annodbg \ +docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0400/graph.primary.small.dbg \ + -a 0400/annotation.clean.row_diff_brwt.annodbg \ --query-mode matches \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ From 4c01d289bc8cc7137dcc239be7dd80b1444d6980 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:42:47 +0200 Subject: [PATCH 14/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 637cb69..8d69661 100644 --- a/README.md +++ b/README.md @@ -219,7 +219,7 @@ metagraph query -i 0400/graph.primary.small.dbg \ docker pull ghcr.io/ratschlab/metagraph:master ``` -Followed by a query on chunk `0001` using the command +Followed by a query on chunk `0400` using the command ```sh docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0400/graph.primary.small.dbg \ -a 0400/annotation.clean.row_diff_brwt.annodbg \ From 16d1022ffae9653f70a3eb11b2fba62f12f67598 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:42:56 +0200 Subject: [PATCH 15/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 8d69661..b270516 100644 --- a/README.md +++ b/README.md @@ -195,7 +195,7 @@ MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) loc ```sh aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --recursive ``` -Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under `examples/100_studies_short.fq`. +Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). #### Conda ```sh From a2bdf8715c1b8cc09e05a12c6b2045275e2733dd Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Thu, 17 Apr 2025 17:43:04 +0200 Subject: [PATCH 16/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index b270516..0886aa4 100644 --- a/README.md +++ b/README.md @@ -193,7 +193,7 @@ Then, it will save the resulting file in the S3. When all chunks are processed, MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows: ```sh -aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --recursive +aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . ``` Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). From dda016dbe70c71bb48f4900d6000cc954ef91bb4 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Tue, 22 Apr 2025 14:26:06 +0200 Subject: [PATCH 17/23] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 0886aa4..ef6c02a 100644 --- a/README.md +++ b/README.md @@ -189,7 +189,7 @@ metagraph query -i graph.primary.small.dbg \ Then, it will save the resulting file in the S3. When all chunks are processed, a dedicated script will merge the results in a single file and send you a notification. -## Instructions for offline usage +## Instructions for local usage MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows: ```sh From b317707e19546a4633d25399baf427f0fd565a45 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Tue, 22 Apr 2025 17:59:36 +0200 Subject: [PATCH 18/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 834e93c..518a03a 100644 --- a/README.md +++ b/README.md @@ -193,7 +193,7 @@ Then, it will save the resulting file in the S3. When all chunks are processed, MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows: ```sh -aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . +aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --no-sign-request --region eu-central-2 ``` Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). From 0ea65e5a640d5b70ce7ae5dced98d12c417739b5 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Wed, 23 Apr 2025 09:33:55 +0200 Subject: [PATCH 19/23] Update README.md --- README.md | 17 ----------------- 1 file changed, 17 deletions(-) diff --git a/README.md b/README.md index 518a03a..3f64c05 100644 --- a/README.md +++ b/README.md @@ -197,23 +197,6 @@ aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --no-sign- ``` Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). -#### Conda -```sh -conda install -c bioconda -c conda-forge metagraph -conda activate metagraph -``` - -Followed by a query on chunk `0400` using the command -```sh -metagraph query -i 0400/graph.primary.small.dbg \ - -a 0400/annotation.clean.row_diff_brwt.annodbg \ - --query-mode matches \ - --num-top-labels 10 \ - --min-kmers-fraction-label 0 \ - --min-kmers-fraction-graph 0 \ - examples/100_studies_short.fq -``` - #### Docker ```sh docker pull ghcr.io/ratschlab/metagraph:master From 8e2c2e8cef5ae332ba92b5dfbe5aba1e6f9a8a4e Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Wed, 23 Apr 2025 09:36:26 +0200 Subject: [PATCH 20/23] Update README.md --- README.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 3f64c05..cc746db 100644 --- a/README.md +++ b/README.md @@ -204,13 +204,14 @@ docker pull ghcr.io/ratschlab/metagraph:master Followed by a query on chunk `0400` using the command ```sh +git clone https://github.com/ratschlab/metagraph-open-data.git docker run -v ${MNTDIR}:/mnt ghcr.io/ratschlab/metagraph:master query -i 0400/graph.primary.small.dbg \ -a 0400/annotation.clean.row_diff_brwt.annodbg \ --query-mode matches \ --num-top-labels 10 \ --min-kmers-fraction-label 0 \ --min-kmers-fraction-graph 0 \ - examples/100_studies_short.fq + metagraph-open-data/examples/100_studies_short.fq ``` replacing `${MNTDIR}` with the local mount path. From e7e81af5819993c9f09972137229284716994990 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Sun, 27 Apr 2025 11:28:16 +0200 Subject: [PATCH 21/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index cc746db..8553100 100644 --- a/README.md +++ b/README.md @@ -191,10 +191,10 @@ Then, it will save the resulting file in the S3. When all chunks are processed, ## Instructions for local usage -MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [`s3://metagraph-data-public`](s3://metagraph-data-public). For example, chunk `0400` can be downloaded to a working directory as follows: -```sh -aws s3 sync s3://metagraph-data-public/all_sra/data/metagenome/0400 . --no-sign-request --region eu-central-2 -``` +MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) locally for offline use on a Linux or a Mac host using the commands below. Search indexes can be downloaded from [s3://metagraph](https://metagraph.s3.amazonaws.com/index.html). For example, chunk `0400` can be downloaded to a working directory as follows: + + aws s3 sync s3://metagraph/all_sra/data/metagenome/0400 . --no-sign-request --region eu-central-2 + Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). #### Docker From 88832641e483c23efca7f31cb11813054c9c2a36 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Sun, 27 Apr 2025 11:28:34 +0200 Subject: [PATCH 22/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 8553100..62e1237 100644 --- a/README.md +++ b/README.md @@ -197,6 +197,12 @@ MetaGraph can be [installed](https://github.com/ratschlab/metagraph#Install) loc Currently, chunks numbered `0001` through to `0400` are available for download. The example query file is located in this repository under [`examples/100_studies_short.fq`](https://github.com/ratschlab/metagraph-open-data/blob/main/examples/100_studies_short.fq). +Alternatively, you can use [Mountpoint for Amazon S3](https://docs.aws.amazon.com/AmazonS3/latest/userguide/mountpoint.html) ([installation guide](https://docs.aws.amazon.com/AmazonS3/latest/userguide/mountpoint-installation.html)) to get direct access to the dataset through the local file system interface: + + mkdir mnt + mount-s3 metagraph mnt --no-sign-request + +After this, e.g. the chunk `0400` will be accessible in the local filesystem at `mnt/all_sra/data/metagenome/0400`. This method should be preferred in environments with a very high internet throughput (i.e. exceeding disk read/write speed), such as clusters, because it allows MetaGraph CLI to download data directly into RAM, bypassing staging on the disk that would otherwise be a bottleneck. #### Docker ```sh docker pull ghcr.io/ratschlab/metagraph:master From 336a7dac31a7bf4257938545449c382a2f603f39 Mon Sep 17 00:00:00 2001 From: Harun Mustafa Date: Sun, 27 Apr 2025 11:28:45 +0200 Subject: [PATCH 23/23] Update README.md Co-authored-by: Oleksandr Kulkov --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 62e1237..6121902 100644 --- a/README.md +++ b/README.md @@ -203,7 +203,9 @@ Alternatively, you can use [Mountpoint for Amazon S3](https://docs.aws.amazon.co mount-s3 metagraph mnt --no-sign-request After this, e.g. the chunk `0400` will be accessible in the local filesystem at `mnt/all_sra/data/metagenome/0400`. This method should be preferred in environments with a very high internet throughput (i.e. exceeding disk read/write speed), such as clusters, because it allows MetaGraph CLI to download data directly into RAM, bypassing staging on the disk that would otherwise be a bottleneck. -#### Docker +### Docker + +You can install the MetaGraph CLI tool with the following command: ```sh docker pull ghcr.io/ratschlab/metagraph:master ```