# QIIME2 Tools on galaxy **URL:** \ **Category:** Technical Support\ **Tags:** install, docker, import\ **Created:** [April 5, 2023, 10:43am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027 "2023-04-05T10:43:14Z")\ **Posts on this page:** 17\ **Page:** 1
**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 5, 2023, 10:43am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/1 "2023-04-05T10:43:14Z")
Hello, My first time to setup a Galaxy Docker with QIIME-2 Tools as per the tutorial to work through some of my data. All appeared working-I could upload fasq.gz and see the highlights of the fastq files. But, The galaxy Docker interface created lacked features I am familiar with on the actual galaxy: creating new history and workflow are lacking etc. When I started to import to QIIME2 formats/artifacts via QIIME2 Tools, the process could not be executed and fails (immediate red color) (I first created collections where all samples had their own respective pairs of reverse and forward sequence files). I went back to the container on the docker, refreshed/restarted the image( [Quay](http://quay.io/qiime2/q2galaxy:latest)). I know these are trivial for so many people :)….but could you guys walk me through these? I appreciate your help ---
**Author:** ![gregcaporaso](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gregcaporaso/32/17769_2.png) [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Post date:** [April 6, 2023, 6:08pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/3 "2023-04-06T18:08:18Z")
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**Author:** ![Oddant1](https://forum.qiime2.org/user_avatar/forum.qiime2.org/oddant1/32/17130_2.png) [@Oddant1](https://forum.qiime2.org/u/Oddant1)\ **Post date:** [April 7, 2023, 6:32pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/4 "2023-04-07T18:32:46Z")
Hello @Wossata, can you post some screenshots of what your Galaxy interface looks like and some example error messages from the processes that failed? Thank you. ---
**Author:** ![cherman2](https://forum.qiime2.org/user_avatar/forum.qiime2.org/cherman2/32/17129_2.png) [@cherman2](https://forum.qiime2.org/u/cherman2)\ **Post date:** [April 7, 2023, 7:01pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/5 "2023-04-07T19:01:18Z")
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**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 8, 2023, 3:58pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/6 "2023-04-08T15:58:53Z")
Unexpected error importing data: stat: path should be string, bytes, os.PathLike or integer, not list ☹ Traceback (most recent call last): File "/export/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/bin/q2galaxy", line 11, in sys.exit(root()) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/click/core.py", line 829, in **call** return self.main(\*args, \*\*kwargs) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return \_process\_result(sub\_ctx.command.invoke(sub\_ctx)) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, \*\*ctx.params) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(\*args, \*\*kwargs) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/q2galaxy/ **main**.py", line 90, in run builtin\_runner(action, config) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 24, in builtin\_runner tool(inputs, stdio=stdio) File "/tool\_deps/_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 43, in import\_data artifact = import\_name\_data(type, format_, files\_to\_move, File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/q2galaxy/core/drivers/stdio.py", line 38, in wrapped return function(\*args, \*\*kwargs) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/q2galaxy/core/drivers/builtins.py", line 84, in _import\_name\_data qiime2.util.duplicate(src, os.path.join(dir_, dst)) File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/site-packages/qiime2/util.py", line 77, in duplicate if os.path.isdir(src): File "/tool\_deps/\_conda/envs/mulled-v1-d2fbd9e406e52f729baea46fa009d86f67fd285aefb55846f62ec86080bf4cab/lib/python3.8/genericpath.py", line 42, in isdir st = os.stat(s) TypeError: stat: path should be string, bytes, os.PathLike or integer, not list ---
**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 8, 2023, 3:59pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/7 "2023-04-08T15:59:04Z")
Hi @Oddant1 thanks for the interest. I have attached screenshots: once data is uploaded (which shows the interface I was refereeing in my first question that you can not create or add 'history' for example). The second and third are once QIIME2 Tools is used to import and convert to artifacts. ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/0/05c7d29c16bf3cbf9a7519f38a655657521b6708.jpeg) ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/4/4c76a4e79b2fff97c46b3b1229d3cf2b62b512c9.jpeg) ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/c/c0aa8d4af21e07d96006afddd5efe183c27b7098.jpeg) Many Thanks Again ---
**Author:** ![gregcaporaso](https://forum.qiime2.org/user_avatar/forum.qiime2.org/gregcaporaso/32/17769_2.png) [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)\ **Post date:** [April 10, 2023, 6:37pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/8 "2023-04-10T18:37:13Z")
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**Author:** ![Oddant1](https://forum.qiime2.org/user_avatar/forum.qiime2.org/oddant1/32/17130_2.png) [@Oddant1](https://forum.qiime2.org/u/Oddant1)\ **Post date:** [April 10, 2023, 10:20pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/9 "2023-04-10T22:20:36Z")
Thank you @Wossata. The issue here appears to be that your data is already paired off. Qiime importing does not expect the data to be paired, it will pair it off on its own. If you give the import command the same data but unpaired that should work. Does that make sense? ---
**Author:** ![Oddant1](https://forum.qiime2.org/user_avatar/forum.qiime2.org/oddant1/32/17130_2.png) [@Oddant1](https://forum.qiime2.org/u/Oddant1)\ **Post date:** [April 10, 2023, 10:21pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/10 "2023-04-10T22:21:16Z")
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**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 11, 2023, 6:53am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/11 "2023-04-11T06:53:42Z")
hi @Oddant1, thanks for the help. Yes, I am able to use QIIME2 Tools for galaxy when I run samples one by one and when I do not make pairs of my own in collection (looking to a way to use for all my data/samples). ---
**Author:** ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)\ **Post date:** [April 11, 2023, 5:07pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/12 "2023-04-11T17:07:45Z")
Hi @Wossata! You can still use all of your samples in the collection, it just can't be a _paired_ collection. I realize this is different from most Galaxy workflows which will make use of that pairing info, but the QIIME 2 file formats expect a particular naming scheme and will work out what is the forward and reverse reads from that. Once it's in the QZA you are good to go and everything will end up working like a paired-collection, just handled automatically. ---
**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 13, 2023, 10:20am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/13 "2023-04-13T10:20:55Z")
Hi @ebolyen @Oddant1 Thanks for the above tips. q2galaxy works fine as long I upload one sample with r1 & r2. Rule-based uploading is appearing to be an issue as my data has no URL associated to it (uploading locally). In building rules as per the tutorial, I put column "A" as list identifier, however, “file path” or anything to that effect is not available for column B (source identifier) (in the dropdown menu). Available options are URL, type, genome, Tag, etc. Someone from last year had the same issue in this thread ([galaxy qiime 2 tools import fastq data - #5 by sdavid](https://forum.qiime2.org/t/galaxy-qiime-2-tools-import-fastq-data/24355/5)) ((couldn't see if answered) I simply used "url" option to see if miracle happens ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/b/bb6848f4dc613efecb7399be8965da72d79e0809.jpeg) ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/8/88d86c9aa237d2415c30d5deee6ae3bd29fbbced.jpeg) Any means to fix this will be greatly appreciated ---
**Author:** ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)\ **Post date:** [April 13, 2023, 5:07pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/14 "2023-04-13T17:07:24Z")
Hi @Wossata, That's close, but you need the 3rd tab instead of the 4th one. It should end up looking something like this: ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/6/6b9ac4cdb1e4d10d7a7d53ab0fcb4891870b963a.png) ---
**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 17, 2023, 11:21am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/15 "2023-04-17T11:21:58Z")
@ebolyen, @Oddant1, Hi Evan, I just could not pass that stage in all three tabs (regular, collections, or rule based in galaxy) when I used all my samples in collection. Again, I can fully operate with qiime2 tools and all on one sample with (r and f sequence reads). Wanted to check one last time if there is way around it? apologies guys 🙂 ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/e/e430fe55076edac542fc590e774015dc040f221a.jpeg) ![image](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/2X/c/c1fec3496065bd8f9e79225d6735dd746e3bce6d.jpeg) ---
**Author:** ![ebolyen](https://forum.qiime2.org/user_avatar/forum.qiime2.org/ebolyen/32/11_2.png) [@ebolyen](https://forum.qiime2.org/u/ebolyen)\ **Post date:** [April 17, 2023, 4:53pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/16 "2023-04-17T16:53:52Z")
Hey @Wossata, I think you basically did it right! We see a good error message now on the right: `Duplicate samples in forward reads: {'J5305'}` I expect you have a resequenced sample with a different barcode segment in the filename or something like that. If you create the collection, but skip the duplicated file, the import should succeed! ---
**Author:** ![Wossata](https://forum.qiime2.org/letter_avatar_proxy/v4/letter/w/ad7895/32.png) [@Wossata](https://forum.qiime2.org/u/Wossata)\ **Post date:** [April 18, 2023, 7:45am UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/17 "2023-04-18T07:45:50Z")
It finally worked after renaming all samples (the first name/after the fourth underscore to the left to be exact) has been causing a problem of "duplication". Much appreciated @ebolyen ! ---
**Author:** ![system](https://forum-qiime2-org.s3.dualstack.us-west-2.amazonaws.com/original/3X/2/1/21af5fe23cb6f4579467c66a9ed94e55274ca7bd.svg) [@system](https://forum.qiime2.org/u/system)\ **Post date:** [May 19, 2023, 1:46pm UTC](https://forum.qiime2.org/t/qiime2-tools-on-galaxy/26027/18 "2023-05-19T13:46:27Z")
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