# Nextflow installation with micromamba seems broken

**URL:** <https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165>\
**Category:** Ask for help\
**Created:** [September 9, 2024, 7:55am UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165 "2024-09-09T07:55:06Z")\
**Posts on this page:** 5\
**Page:** 1

<div class="post-metadata">

**Author:** ![Gullumluvl](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/gullumluvl/32/1050_2.png) [@Gullumluvl](https://community.seqera.io/u/Gullumluvl)\
**Post date:** [September 9, 2024, 7:55am UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165/1 "2024-09-09T07:55:06Z")

</div>

Hi there!

I get strange errors when calling `nextflow run helloworld.nf` on two different hosts where I installed it via micromamba.

On the Debian 12 it says:

```auto
library initialization failed - unable to allocate file descriptor table - out of memoryUnable to initialize nextflow environment

```

(Same error when trying `nextflow info`).

On the CentOS 7.9 it says:

```auto
N E X T F L O W ~ version 0.24.2
Launching `src/helloworld.nf` [high_mirzakhani] - revision: b1230ea5c8
ERROR ~ Unknown process directive: `path`

Did you mean of these?
        each

 -- Check script 'helloworld.nf' at line: 5 or see '.nextflow.log' file for more details

```

But `nextflow info` works.

To me it looks like the Java/Groovy dependencies that should have been installed by micromamba are not used.

Steps to reproduce:

1. Install micromamba:

2. `micromamba create -n testnextflow nextflow` which apparently installs openjdk.

3. `micromamba activate testnextflow`

4. Save the tutorial workflow from here: [Your first script — Nextflow v24.08.0-edge documentation](https://www.nextflow.io/docs/latest/your-first-script.html) to `helloworld.nf`

5. `nextflow run helloworld.nf`

I don’t know if it’s a nextflow problem or a micromamba problem.

I have succeeded in installing nextflow using the recommended default method and also using `conda` with `--solver libmamba`.

I suppose the environment set up by the micromamba executable is incorrect.

Any ideas?

Thanks in advance!

---

<div class="post-metadata">

**Author:** ![kenibrewer](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/kenibrewer/32/963_2.png) [@kenibrewer](https://community.seqera.io/u/kenibrewer)\
**Post date:** [September 9, 2024, 9:21pm UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165/2 "2024-09-09T21:21:54Z")

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Hi @Gullumluvl !

The Debian 12 installation is definitely a broken Nextflow install. Maybe check to make sure that you have a compatible java install?

The CentOS 7.9 nextflow looks like it’s installed correctly but you might have a bug in your `helloworld.nf`. The unknown process directive `path` is usually a syntax problem. Could be a missing comma or an unmatched `{` somewhere.

---

<div class="post-metadata">

**Author:** ![Gullumluvl](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/gullumluvl/32/1050_2.png) [@Gullumluvl](https://community.seqera.io/u/Gullumluvl)\
**Post date:** [September 10, 2024, 8:24am UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165/3 "2024-09-10T08:24:27Z")

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Hi! Thanks for your reply.

Just answering about the syntax problem on CentOS: it also happens when I do `nextflow run hello` which fetches the workflow remotely; the error is slightly different (stdout is undefined), but it also looks like nextflow or groovy’s required classes are not loaded.

---

<div class="post-metadata">

**Author:** ![Gullumluvl](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/gullumluvl/32/1050_2.png) [@Gullumluvl](https://community.seqera.io/u/Gullumluvl)\
**Post date:** [September 10, 2024, 3:14pm UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165/4 "2024-09-10T15:14:17Z")

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Update:

Not sure what I did because it appears to be working correctly now. Maybe I did not source the .bashrc after installing micromamba, or maybe I should have quit the terminal instead\[1\].

Now the launcher file, such as `$HOME/.nextflow/tmp/launcher/nextflow-one_24.04.4/$HOSTNAME/classpath-8269d21...`  
correctly starts with an environment specific java path, instead of using `/usr/bin/java`.

* * *

1. Still I’m convinced I _had_ setup micromamba, because otherwise the command `micromamba activate testnextflow` would have failed, and also no nextflow executable would have been found. This would need experiments on a fresh install.

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<div class="post-metadata">

**Author:** ![kenibrewer](https://dub1.discourse-cdn.com/flex013/user_avatar/community.seqera.io/kenibrewer/32/963_2.png) [@kenibrewer](https://community.seqera.io/u/kenibrewer)\
**Post date:** [September 10, 2024, 3:18pm UTC](https://community.seqera.io/t/nextflow-installation-with-micromamba-seems-broken/1165/5 "2024-09-10T15:18:28Z")

</div>

Glad you figured it out and thanks for sharing your insights back here. Happy scienc-ing!