From 22fe8ba3ce430a964b433454badc04498fc0a1bc Mon Sep 17 00:00:00 2001 From: misialq Date: Mon, 16 Dec 2024 11:02:05 +0000 Subject: [PATCH] deploy: f316c0e1c0cb6acf3b19c1da235ee3dce91abea6 --- .../chapters/05_interoperability/export.md | 66 ++++++++++++++--- chapters/05_interoperability/export.html | 72 ++++++++++++++++--- searchindex.js | 2 +- 3 files changed, 123 insertions(+), 17 deletions(-) diff --git a/_sources/chapters/05_interoperability/export.md b/_sources/chapters/05_interoperability/export.md index 1348713..ba2e421 100644 --- a/_sources/chapters/05_interoperability/export.md +++ b/_sources/chapters/05_interoperability/export.md @@ -21,7 +21,7 @@ artifacts will contain data in the original format that the underlying tool uses export data from QIIME 2 and connect it with other tools. ```{warning} -QIIME 2 does not yet support exporting data from the cache. This means that you will need to manually copy the data from the +QIIME 2 does not yet support exporting data from the cache (see below). This means that you will need to manually copy the data from the cache directory to a location where you can access it with other tools. In our examples, the cache directory is located directly in the working directory and that is where we will copy the data from. Keep in mind that you should never temper with the files in the cache directory directly, as this may lead to broken artifacts and failed analyses. @@ -31,23 +31,73 @@ in the cache directory directly, as this may lead to broken artifacts and failed If you have used Kraken 2 to [classify your reads](kraken-reads), you can export the resulting reports from the corresponding QIIME 2 artifact and visualize them with [Pavian](https://github.com/fbreitwieser/pavian) which will allow you to explore the taxonomic composition of your samples in an interactive way. To export the Kraken 2 reports, you can use the following commands: + +`````{tab-set} +````{tab-item} Direct export +Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of +the issue [here](https://github.com/qiime2/qiime2/issues/822). +```` + +````{tab-item} Workaround 1: without using QIIME ```bash UUID=$(cat ./cache/keys/kraken_reports_reads | grep 'data' | awk '{print $2}') -mkdir exported_reports -cp -r ./cache/data/$UUID/data/* exported_reports/ +mkdir ./exported_reports +cp -r ./cache/data/$UUID/data/* ./exported_reports/ ``` This will find the UUID of the reports artifact, use it to locate the data within the cache directory, create a directory -for the exported data and copy the files from the cache into it. You can then use those files (within the `exported_reports` -directory) with Pavian. To give it a quick try, navigate to [Pavian's demo site](https://fbreitwieser.shinyapps.io/pavian/) -and upload the exported files. +for the exported data and copy the files from the cache into it. +```` + +````{tab-item} Workaround 2: with QIIME +```bash +qiime tools cache-fetch \ + --cache ./cache \ + --key kraken_reports_reads \ + --output-path ./kraken_reports_reads.qza + +qiime tools export \ + --input-path ./kraken_reports_reads.qza \ + --output-path ./exported_reports +``` +This will first fetch the reports artifact from the cache and then export it to the `exported_reports` directory. +```` +````` + +Once you got the data into the `exported_reports` directory, you can then use those with Pavian. +To give it a quick try, navigate to [Pavian's demo site](https://fbreitwieser.shinyapps.io/pavian/) and upload the exported files. ## Microbial pangenomics with Anvi'o Another suite of tools you may be familiar with is the [Anvi'o](http://anvio.org/) platform. One of the workflows that Anvi'o provides is the microbial pangenomics analysis, which can be used to explore the gene clusters within your samples. You could export the MAGs obtained from the [binning step](mag-recovery) and use them as input to the `anvi-pan-genome` workflow, as described [here](https://merenlab.org/2016/11/08/pangenomics-v2/). To export the MAGs, you can use the following command: +`````{tab-set} +````{tab-item} Direct export +Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of +the issue [here](https://github.com/qiime2/qiime2/issues/822). +```` + +````{tab-item} Workaround 1: without using QIIME ```bash UUID=$(cat ./cache/keys/mags | grep 'data' | awk '{print $2}') -mkdir exported_mags -cp -r ./cache/data/$UUID/data/* exported_mags/ +mkdir ./exported_mags +cp -r ./cache/data/$UUID/data/* ./exported_mags/ +``` +This will find the UUID of the MAGs artifact, use it to locate the data within the cache directory, create a directory +for the exported data and copy the files from the cache into it. +```` + +````{tab-item} Workaround 2: with QIIME +```bash +qiime tools cache-fetch \ + --cache ./cache \ + --key mags \ + --output-path ./mags.qza + +qiime tools export \ + --input-path ./mags.qza \ + --output-path ./exported_mags ``` +This will first fetch the MAGs artifact from the cache and then export it to the `exported_mags` directory. +```` +````` diff --git a/chapters/05_interoperability/export.html b/chapters/05_interoperability/export.html index 5662833..076e75d 100644 --- a/chapters/05_interoperability/export.html +++ b/chapters/05_interoperability/export.html @@ -351,7 +351,7 @@

Contents

export data from QIIME 2 and connect it with other tools.

Warning

-

QIIME 2 does not yet support exporting data from the cache. This means that you will need to manually copy the data from the +

QIIME 2 does not yet support exporting data from the cache (see below). This means that you will need to manually copy the data from the cache directory to a location where you can access it with other tools. In our examples, the cache directory is located directly in the working directory and that is where we will copy the data from. Keep in mind that you should never temper with the files in the cache directory directly, as this may lead to broken artifacts and failed analyses.

@@ -361,15 +361,42 @@

Visualizing Kraken 2 reports with Pavianclassify your reads, you can export the resulting reports from the corresponding QIIME 2 artifact and visualize them with Pavian which will allow you to explore the taxonomic composition of your samples in an interactive way. To export the Kraken 2 reports, you can use the following commands:

+
+ +
+

Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of +the issue here.

+
+ +
UUID=$(cat ./cache/keys/kraken_reports_reads | grep 'data' | awk '{print $2}')
-mkdir exported_reports
-cp -r ./cache/data/$UUID/data/* exported_reports/
+mkdir ./exported_reports
+cp -r ./cache/data/$UUID/data/* ./exported_reports/

This will find the UUID of the reports artifact, use it to locate the data within the cache directory, create a directory -for the exported data and copy the files from the cache into it. You can then use those files (within the exported_reports -directory) with Pavian. To give it a quick try, navigate to Pavian’s demo site -and upload the exported files.

+for the exported data and copy the files from the cache into it.

+
+ +
+
qiime tools cache-fetch \
+    --cache ./cache \
+    --key kraken_reports_reads \
+    --output-path ./kraken_reports_reads.qza
+
+qiime tools export \
+    --input-path ./kraken_reports_reads.qza \
+    --output-path ./exported_reports
+
+
+

This will first fetch the reports artifact from the cache and then export it to the exported_reports directory.

+
+
+

Once you got the data into the exported_reports directory, you can then use those with Pavian. +To give it a quick try, navigate to Pavian’s demo site and upload the exported files.

Microbial pangenomics with Anvi’o#

@@ -377,11 +404,40 @@

Microbial pangenomics with Anvi’obinning step and use them as input to the anvi-pan-genome workflow, as described here. To export the MAGs, you can use the following command:

+
+ +
+

Support for extracting data out of the cache is not yet available but is coming soon! You can track the progress of +the issue here.

+
+ +
UUID=$(cat ./cache/keys/mags | grep 'data' | awk '{print $2}')
-mkdir exported_mags
-cp -r ./cache/data/$UUID/data/* exported_mags/
+mkdir ./exported_mags
+cp -r ./cache/data/$UUID/data/* ./exported_mags/
+
+
+

This will find the UUID of the MAGs artifact, use it to locate the data within the cache directory, create a directory +for the exported data and copy the files from the cache into it.

+
+ +
+
qiime tools cache-fetch \
+    --cache ./cache \
+    --key mags \
+    --output-path ./mags.qza
+
+qiime tools export \
+    --input-path ./mags.qza \
+    --output-path ./exported_mags
+

This will first fetch the MAGs artifact from the cache and then export it to the exported_mags directory.

+
+

diff --git a/searchindex.js b/searchindex.js index 9cc9529..f35818c 100644 --- a/searchindex.js +++ b/searchindex.js @@ -1 +1 @@ -Search.setIndex({"alltitles": {"Annotate orthologs against eggNOG database": [[13, "annotate-orthologs-against-eggnog-database"]], "Approach 1: Kraken 2": [[11, "approach-1-kraken-2"]], "Approach 2: Kaiju": [[11, "approach-2-kaiju"]], "Assemble contigs with MEGAHIT": [[8, "assemble-contigs-with-megahit"]], "Bin contigs with MetaBAT": [[8, "bin-contigs-with-metabat"]], "Compare MinHash signatures": [[6, "compare-minhash-signatures"]], "Compute MinHash signatures with Sourmash": [[6, "compute-minhash-signatures-with-sourmash"]], "Contig QC with QUAST": [[8, "contig-qc-with-quast"]], "Data retrieval": [[0, null]], "Dereplicate MAGs": [[6, "dereplicate-mags"]], "EggNOG search using Diamond aligner": [[13, "eggnog-search-using-diamond-aligner"]], "Estimate MAG abundance": [[5, "estimate-mag-abundance"]], "Evaluate bins with BUSCO": [[8, 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