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2018-10-31 12:18:47 -0600 marked best answer error in 22.5: aclssl.so undefined symbol

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
2018-10-30 13:07:10 -0600 commented answer error in 22.5: aclssl.so undefined symbol

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

2018-10-30 13:04:13 -0600 edited question error in 22.5: aclssl.so undefined symbol

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

2018-10-29 11:26:45 -0600 asked a question error in 22.5: aclssl.so undefined symbol

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

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2017-10-21 09:31:54 -0600 edited question problems with genbank file

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

2017-10-21 09:31:02 -0600 marked best answer Draft genome & pathologic

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, ... ?)

2017-10-21 09:28:35 -0600 marked best answer Changing the database in lisp expression

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.

2017-10-21 09:11:40 -0600 asked a question problems with genbank file

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

2017-09-19 02:37:24 -0600 asked a question Draft genome & pathologic

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

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2017-08-24 07:11:21 -0600 answered a question Changing the database in lisp expression

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

2017-08-24 02:06:20 -0600 commented answer Changing the database in lisp expression

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

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2017-08-24 01:59:37 -0600 edited question Changing the database in lisp expression

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

2017-08-23 10:34:49 -0600 asked a question Changing the database in lisp expression

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

2017-08-23 10:18:17 -0600 marked best answer PythonCyc: obtain only children classes

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?

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2017-08-20 09:07:37 -0600 commented answer PythonCyc: obtain only children classes

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

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2017-08-16 11:55:36 -0600 asked a question PythonCyc: obtain only children classes

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

2017-08-15 05:34:05 -0600 answered a question Accessing the pathway hierarchy

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

2017-08-15 05:10:58 -0600 commented answer Accessing the pathway hierarchy

Thanks your answer helped a lot!

2017-08-15 05:10:10 -0600 marked best answer Accessing the pathway hierarchy

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?

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2017-07-14 08:01:28 -0600 asked a question Accessing the pathway hierarchy

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

2017-05-18 08:40:31 -0600 marked best answer access pathologic via api

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?

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2017-05-18 08:40:07 -0600 answered a question access pathologic via api

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

2017-05-17 05:46:02 -0600 asked a question access pathologic via api

access pathologic via api Is it possible to access pathologic via an API? Would like to create draft models via the path

2017-02-23 08:41:24 -0600 answered a question How to publish my PGDB

any answers to that?