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I just installed the latest version 22.5 of pathway tools. But when I try to start, I'm getting this error:

pathway-tools
; Foreign loading libcrypto.so.1.0.0.
; Foreign loading libcrypto.so.10.
; Foreign loading libcrypto.so.
; Foreign loading libssl.so.1.0.0.
; Foreign loading libssl.so.10.
; Foreign loading libssl.so.
; Foreign loading sys:aclssl.so.
An unhandled error occurred during initialization:
Loading sys:aclssl.so failed with error:
pathway-tools/aic-export/pathway-tools/ptools/22.5/exe/aclssl.so: undefined symbol: CRYPTO_set_locking_callback.
[physical pathname is
pathway-tools/aic-export/pathway-tools/ptools/22.5/exe/aclssl.so]

I'm running debian 10 (testing, buster) 4.18.0-2-amd64 and installed libxm4 as mentioned in the readme.

ldd -v aic-export/pathway-tools/ptools/22.5/exe/aclssl.so 

linux-vdso.so.1 (0x00007fff1ffce000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007f6efd983000)
librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00007f6efd979000)
libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00007f6efd7e5000)
libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007f6efd7e0000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007f6efd623000)
/lib64/ld-linux-x86-64.so.2 (0x00007f6efdbcf000)

Version information:
aic-export/pathway-tools/ptools/22.5/exe/aclssl.so:
    libdl.so.2 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libdl.so.2
    libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libpthread.so.0:
    ld-linux-x86-64.so.2 (GLIBC_2.2.5) => /lib64/ld-linux-x86-64.so.2
    ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
    libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/librt.so.1:
    libpthread.so.0 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libpthread.so.0
    libpthread.so.0 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libpthread.so.0
    libpthread.so.0 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libpthread.so.0
    libc.so.6 (GLIBC_2.14) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.3.2) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libm.so.6:
    ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
    libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libdl.so.2:
    ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2
    libc.so.6 (GLIBC_PRIVATE) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.4) => /lib/x86_64-linux-gnu/libc.so.6
    libc.so.6 (GLIBC_2.2.5) => /lib/x86_64-linux-gnu/libc.so.6
/lib/x86_64-linux-gnu/libc.so.6:
    ld-linux-x86-64.so.2 (GLIBC_2.3) => /lib64/ld-linux-x86-64.so.2
    ld-linux-x86-64.so.2 (GLIBC_PRIVATE) => /lib64/ld-linux-x86-64.so.2

thanks for you answer! I included the shared object dependencies in my post! But I wouldn't call debian 10 an 'ancient l

error in 22.5: aclssl.so undefined symbol I just installed the latest version 22.5 of pathway tools. But when I try to s

error in 22.5: aclssl.so undefined symbol I just installed the latest version 22.5 of pathway tools. But when I try to s

problems with genbank file I have problems creating a reconstruction with pathwaystools (21.0) when it comes to this gen

What do you think is the best practice when reconstructing a metabolic network using pathwaytools/pathologic and having only a draft genome?

Draft genomes can have a lot of unconnected contigs. Pathologic needs a annotation file as input but the annotation of draft genomes is also not always trustworthy.

I'm interested in this because I encountered different results of predicted reactions and pathways when I created two pgdbs out of the same genome but using two distinct annotation files done by different prokka versions. I know that the pathway prediction algorithm is doing some kind of text mining with the annotation file but it is also using the raw sequence data to annotate gene function itself.

What is the balance between text mining and redoing the annotation? Can this be changed for draft genomes? Do you have recommendation for annotation software which works best with pathologic? (prokka, rast, ... ?)

I'm using sendQueryToPTools in PythonCyc in order to be able to use lisp expressions.

I can get the class of a pathway

pythoncyc.sendQueryToPTools("(get-instance-direct-types '|GLYSYN-PWY|)")

But this is not working for all pathways

pythoncyc.sendQueryToPTools("(get-instance-direct-types '|PWY-6120|)")

PToolsError: An internal error occurred in the running Pathway Tools application: :error Object "PWY-6120" is not coercible to a frame for KB ECOBASE

I assume it is caused by the database (ECOBASE). How can switch to METACYC?

PS.: I tried pythoncyc.select_organism('meta') but it is returning a pdgb object and seems to have no influence on the lisp query.

problems with genbank file I have problems creating a reconstruction with pathwaystools (21.0) when it comes to this gen

Draft genome & pathologic What do you think is the best practice when reconstructing a metabolic network using pathw

I found a workaround by starting the pathwaytools executable with metacyc as the default pgdb: pathway-tools -python-lo

Unfortunately, this is not working. I used select_organism before sending the lisp query. I included this to the questio

Changing the database in lisp expression I'm using sendQueryToPTools in PythonCyc in order to be able to use lisp expres

Changing the database in lisp expression I'm using sendQueryToPTools in PythonCyc in order to be able to use lisp expres

Using get_class_all_subs I get access all subclasses with the PythonCyc API. How can I get only the direct subclasses (children) without the other deeper subclasses? Is there something like a parent or children attribute for a class?

Great this is working thank you! Using your first command, I can already return only frame names in pythoncyc. Do you kn

PythonCyc: obtain only children classes Using get_class_all_subs I get access all subclasses with the PythonCyc API. Ho

In addition to this, I tried the API to get informations about the hierarchy. Using PythonCyc in the following: import

Thanks your answer helped a lot!

I'm wondering if there is a way to read out the metacyc pathway hierarchy?

More precisely, I want to get e.g. all pathways from class Detoxification->Acid Resistance. Could this be done via the API or somehow else?

Accessing the pathway hierarchy I'm wondering if there is a way to read out the metacyc pathway hierarchy? More precise

Is it possible to access pathologic via an API? Would like to create draft models via the pathologic algorithms without using the graphical interface. Could this be done?

Thanks for pointing this out! So I defined organism-params.dat and genetic-elements.dat in a folder called dir_with_fil

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any answers to that?