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fix a few links (#203)
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* fix a few links

* a few more

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Co-authored-by: Timo Sachsenberg <[email protected]>
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cbielow and timosachsenberg authored Sep 15, 2023
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2 changes: 1 addition & 1 deletion docs/introduction/entry-points-to-openms.md
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Expand Up @@ -36,7 +36,7 @@ The following entry points for OpenMS and its TOPP tools are available for users
:::

:::{grid-item-card} {fab}`python;sd-text-info fa-xl` **pyOpenMS** <br/> Use the pyOpenMS python library to rapidly prototype methods and scripts
:link: https://pyopenms.readthedocs.io/en/latest/installation.html
:link: https://pyopenms.readthedocs.io/en/latest/user_guide/installation.html
:link-type: url
:class-title: flex

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2 changes: 1 addition & 1 deletion docs/run-workflows-with-openms-tools/knime/installation.md
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Expand Up @@ -54,7 +54,7 @@ Download Introduction to OpenMS in KNIME [user tutorial](../../tutorials-and-qui
usage of KNIME. See the official [KNIME Getting Started Guide](https://tech.knime.org/knime) for a more in-depth view of
the KNIME functionality besides OpenMS.

If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/c/community-extensions/openms/40).
If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tags/c/community-extensions/38/openms).

## Creating your own Generic KNIME Nodes

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8 changes: 4 additions & 4 deletions docs/run-workflows-with-openms-tools/knime/tutorial.md
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Expand Up @@ -2493,7 +2493,7 @@ Now launch ”Spyder” (python IDE) in the home menu.
### Build instructions
Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/build_from_source.html).
Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/community/build_from_source.html).
### Scripting with pyOpenMS
Expand Down Expand Up @@ -2559,7 +2559,7 @@ for iso in isotopes.getContainer():
print (iso.getMZ(), ":", iso.getIntensity())
```
For further examples and the pyOpenMS data structures please see the following [link](https://pyopenms.readthedocs.io/en/latest/ms_data.html).
For further examples and the pyOpenMS data structures please see the following [link](https://pyopenms.readthedocs.io/en/latest/user_guide/ms_data.html).
### Tool development with pyOpenMS
Expand Down Expand Up @@ -2940,7 +2940,7 @@ You can look up temporary files that are created by OpenMS nodes not connected t
**Q:** I have problem XYZ but it also occurs with other nodes or generally in the KNIME environment/GUI, what should I do?
**A:** This sounds like a general KNIME bug and we advise to search help directly at the KNIME developers. They also provide a [FAQ](https://tech.knime.org/) and a [forum](https://tech.knime.org/forum).
**A:** This sounds like a general KNIME bug and we advise to search help directly at the KNIME developers. They also provide a [FAQ](https://www.knime.com/faq) and a [forum](https://forum.knime.com).
**Q:** After exporting and reading in results into a KNIME table (e.g. with a MzTabExporter and MzTabReader combination) numeric values get rounded (e.g. from scientific notation 4.5e-10 to zero) or are in a different representation than in the underlying exported file!
Expand All @@ -2964,7 +2964,7 @@ You can look up temporary files that are created by OpenMS nodes not connected t
**Q:** Why is my configuration dialog closing right away when I double-click or try to configure it? Or why is my GUI responding so slow?
**A:** If you have any problems with the KNIME GUI or the opening of dialogues under Linux you might be affected by a GTK bug. See the KNIME forum (e.g. [here](https://tech.knime.org/forum/knime-general/ubuntu-1604-slow-performance) or [here](https://tech.knime.org/forum/knime-users/knime-300-crashes-after-splash-screen)) for a discussion and a possible solution. In short: set environment variable by calling `export SWT_GTK3=0` or edit `knime.ini` to make Eclipse use GTK2 by adding the following two lines:
**A:** If you have any problems with the KNIME GUI or the opening of dialogues under Linux you might be affected by a GTK bug. See the KNIME forum (e.g. [here](https://forum.knime.com/t/ubuntu-16-04-slow-performance/4345) or [here](https://forum.knime.com/t/knime-3-0-0-crashes-after-splash-screen/8370)) for a discussion and a possible solution. In short: set environment variable by calling `export SWT_GTK3=0` or edit `knime.ini` to make Eclipse use GTK2 by adding the following two lines:
```xml
–launcher.GTK_version
2
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8 changes: 4 additions & 4 deletions docs/tutorials-and-quickstart-guides/openms-user-tutorial.md
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Expand Up @@ -2492,7 +2492,7 @@ Now launch ”Spyder” (python IDE) in the home menu.
### Build instructions
Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/build_from_source.html).
Instructions on how to build pyOpenMS can be found [online](https://pyopenms.readthedocs.io/en/latest/community/build_from_source.html).
### Scripting with pyOpenMS
Expand Down Expand Up @@ -2558,7 +2558,7 @@ for iso in isotopes.getContainer():
print (iso.getMZ(), ":", iso.getIntensity())
```
For further examples and the pyOpenMS data structures please see the following [link](https://pyopenms.readthedocs.io/en/latest/ms_data.html).
For further examples and the pyOpenMS data structures please see the following [link](https://pyopenms.readthedocs.io/en/latest/user_guide/ms_data.html).
### Tool development with pyOpenMS
Expand Down Expand Up @@ -2939,7 +2939,7 @@ You can look up temporary files that are created by OpenMS nodes not connected t
**Q:** I have problem XYZ but it also occurs with other nodes or generally in the KNIME environment/GUI, what should I do?
**A:** This sounds like a general KNIME bug and we advise to search help directly at the KNIME developers. They also provide a [FAQ](https://tech.knime.org/) and a [forum](https://tech.knime.org/forum).
**A:** This sounds like a general KNIME bug and we advise to search help directly at the KNIME developers. They also provide a [FAQ](https://www.knime.com/faq) and a [forum](https://forum.knime.com).
**Q:** After exporting and reading in results into a KNIME table (e.g. with a MzTabExporter and MzTabReader combination) numeric values get rounded (e.g. from scientific notation 4.5e-10 to zero) or are in a different representation than in the underlying exported file!
Expand All @@ -2963,7 +2963,7 @@ You can look up temporary files that are created by OpenMS nodes not connected t
**Q:** Why is my configuration dialog closing right away when I double-click or try to configure it? Or why is my GUI responding so slow?
**A:** If you have any problems with the KNIME GUI or the opening of dialogues under Linux you might be affected by a GTK bug. See the KNIME forum (e.g. [here](https://tech.knime.org/forum/knime-general/ubuntu-1604-slow-performance) or [here](https://tech.knime.org/forum/knime-users/knime-300-crashes-after-splash-screen)) for a discussion and a possible solution. In short: set environment variable by calling `export SWT_GTK3=0` or edit `knime.ini` to make Eclipse use GTK2 by adding the following two lines:
**A:** If you have any problems with the KNIME GUI or the opening of dialogues under Linux you might be affected by a GTK bug. See the KNIME forum (e.g. [here](https://forum.knime.com/t/ubuntu-16-04-slow-performance/4345) or [here](https://forum.knime.com/t/knime-3-0-0-crashes-after-splash-screen/8370)) for a discussion and a possible solution. In short: set environment variable by calling `export SWT_GTK3=0` or edit `knime.ini` to make Eclipse use GTK2 by adding the following two lines:
```xml
–launcher.GTK_version
2
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2 changes: 1 addition & 1 deletion docs/tutorials/KNIME/KNIME-tutorial.md
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Expand Up @@ -61,7 +61,7 @@ Download Introduction to OpenMS in KNIME [user tutorial](../../tutorials-and-qui
usage of KNIME. See the official [KNIME Getting Started Guide](https://tech.knime.org/knime) for a more in-depth view of
the KNIME functionality besides OpenMS.

If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/c/community-extensions/openms/40).
If you face any issues, please [contact us](/quick-reference/contact-us.md) and specifically for the usage of OpenMS in KNIME, the KNIME community contribution [forum](https://forum.knime.com/tags/c/community-extensions/38/openms).

## Creating your own Generic KNIME Nodes

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