nextPYP

nextPYP: a scalable platform for cryo-EM/ET image analysis
nextPYP is a package for single-particle cryo-EM/ET image analysis developed and maintained by the Bartesaghi Lab.
 
By combining established tools in the field with methods developed in-house, nextPYP produces state-of-the-art results while being user-friendly and scalable to large datasets.
 
Main features
  Ease-of-use: user-friendly, fully-featured web-based GUI with intuitive block-based architecture
 
  End-to-end: convert raw cryo-EM/ET data into high-resolution structures using a single application
 
  Particle picking suite: cellular pattern mining and suite of particle picking tools in 2D and 3D
 
  High-resolution: advanced 3D refinement and classification tools achieve state-of-the-art results
 
  Scalability: small storage footprint and distributed computing allows analysis of large datasets
 
  On-the-fly processing: real-time analysis of micrographs and tilt-series during data acquisition
 
  Portability and compatibility: easy to install and configure, interoperable with external packages
 
  See the Changelog for the latest features.
 
Citing nextPYP
Liu, HF., Zhou, Y., Huang, Q., Piland, J., Jin, W., Mandel, J., Du, X., Martin, J., Bartesaghi, A., nextPYP: a comprehensive and scalable platform for characterizing protein variability in-situ using single-particle cryo-electron tomography. Nat Meth, 20:1909–1919 (2023).

[root@rockylinux9 ~]# lsblk
NAME   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINTS
sda      8:0    0   192G  0 disk
├sda1   8:1    0     1M  0 part
├sda2   8:2    0     1G  0 part /boot
├sda3   8:3    0   128M  0 part [SWAP]
├sda4   8:4    0     1K  0 part
└sda5   8:5    0 190.9G  0 part /
sdb      8:16   0     2T  0 disk
└sdb1   8:17   0     2T  0 part /opt
[root@rockylinux9 ~]#

[root@rockylinux9 ~]# cat /etc/redhat-release
Rocky Linux release 9.8 (Blue Onyx)
 
[root@rockylinux9 ~]# useradd --system --user-group nextpyp
 
[root@rockylinux9 ~]# id nextpyp
uid=984(nextpyp) gid=983(nextpyp) groups=983(nextpyp)
 
[root@rockylinux9 ~]# getent passwd nextpyp
nextpyp:x:984:983::/home/nextpyp:/bin/bash
 
[root@rockylinux9 ~]# ls -l /home/nextpyp                        
ls: cannot access '/home/nextpyp': No such file or directory    <-- ホームディレクトリは作られてないです
 
[root@rockylinux9 ~]#

[root@rockylinux9 ~]# nvidia-smi -L
GPU 0: NVIDIA RTX A2000 (UUID: GPU-23cc3ee7-31d3-a068-2f61-5aa00052d084)
[root@rockylinux9 ~]#

[root@rockylinux9 ~]# dnf install epel-release -y
[root@rockylinux9 ~]# dnf install apptainer wget -y

[root@rockylinux9 ~]# mkdir -p /opt/nextPYP
[root@rockylinux9 ~]# cd /opt/nextPYP
[root@rockylinux9 nextPYP]# wget https://nextpyp.app/files/pyp/latest/install
[root@rockylinux9 nextPYP]# chmod +x ./install

[root@rockylinux9 nextPYP]# mkdir /opt/nextPYP-data
 
[root@rockylinux9 nextPYP]# PYP_USER="nextpyp" PYP_STORAGE="/opt/nextPYP-data" ./install
 :
 :
 :
[root@rockylinux9 nextPYP]#
[root@rockylinux9 nextPYP]# ls -l
total 451812
lrwxrwxrwx. 1 root root        40 Sep 11 02:04 config.toml -> /opt/nextPYP-data/sharedExec/config.toml
-rwxr-xr-x. 1 root root     28349 Jan 24  2026 install
-rw-r--r--. 1 root root      2685 Aug 25  2025 install-rprox
lrwxrwxrwx. 1 root root        23 Sep 11 00:14 local -> /opt/nextPYP-data/local
-rw-r--r--. 1 root root 457850880 May  4 06:12 nextPYP.sif
lrwxrwxrwx. 1 root root        24 Sep 11 00:14 shared -> /opt/nextPYP-data/shared
lrwxrwxrwx. 1 root root        28 Sep 11 00:14 sharedExec -> /opt/nextPYP-data/sharedExec
-rw-r--r--. 1 root root      4321 Apr 26  2025 uninstall
-rw-r--r--. 1 root root   4762456 Sep  5  2025 user-processor
drwxr-xr-x. 2 root root        84 Sep 11 02:04 workflows
[root@rockylinux9 nextPYP]#

[root@rockylinux9 nextPYP]# wget http://localhost:8080 -O -
--2026-09-11 11:11:15--  http://localhost:8080/
Resolving localhost (localhost)... ::1, 127.0.0.1
Connecting to localhost (localhost)|::1|:8080... failed: Connection refused.
Connecting to localhost (localhost)|127.0.0.1|:8080... connected.
HTTP request sent, awaiting response... 200 OK
Length: 353 [text/html]
Saving to: ‘STDOUT’
 
-                                        0%[                                                                           ]       0  --.-KB/s               <!DOCTYPE html>
<html>
<head>
    <meta charset="utf-8">
    <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
    <title>nextPYP</title>
    <link rel="icon" type="image/png" href="favicon.png">
    <script type="text/javascript" src="main.bundle.js"></script>
</head>
<body>
<div id="mmapp"></div>
</body>
</html>
-                                      100%[==========================================================================>]     353  --.-KB/s    in 0s
 
2026-09-11 11:11:15 (76.2 MB/s) - written to stdout [353/353]
 
[root@rockylinux9 nextPYP]#

[root@rockylinux9 ~]# vi /opt/nextPYP/config.toml
 
[pyp]
 
# fast storage for temporary files, ideally local to the compute node
scratch = '/opt/nextPYP-data/scratch'
 
# add folder paths into this list to make your data visible to nextPYP
binds = [
   '/data1',
   '/data2'
]
 :
 :
[root@rockylinux9 ~]#

[root@rockylinux9 ~]# systemctl restart nextPYP.service

[root@rockylinux9 ~]# vi /opt/nextPYP/config.toml
 :
 :
[web]
host = '0.0.0.0'
 :
 :
[root@rockylinux9 ~]#